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Document And Entity Information - shares	9 Months Ended
Document And Entity Information - shares	Sep. 30, 2012	Nov. 02, 2012
Document And Entity Information [Abstract]
Document Type	10-Q
Amendment Flag	false
Document Period End Date	Sep. 28, 2012
Document Fiscal Year Focus	2012
Document Fiscal Period Focus	Q3
Trading Symbol	exel
Entity Registrant Name	EXELIXIS, INC.
Entity Central Index Key	0000939767
Entity Filer Category	Large Accelerated Filer
Current Fiscal Year End Date	--12-28
Entity Common Stock, Shares Outstanding		183,596,930

Condensed Consolidated Balance Sheets - USD ($)
$ in Thousands

Sep. 30, 2012

Dec. 31, 2011

^[1]

ASSETS

Cash and cash equivalents

$ 308,805

$ 74,257

Marketable securities

163,542

120,005

Short-term restricted cash and investments

12,242

Other receivables

2,708

30,190

Prepaid expenses and other current assets

6,098

4,372

Total current assets

493,395

228,824

Restricted cash and investments

27,946

4,199

Long-term investments

162,173

85,260

Property and equipment, net

6,292

8,506

Goodwill

63,684

Other assets

9,123

2,789

Total assets

762,613

393,262

LIABILITIES AND STOCKHOLDERS' EQUITY

Accounts payable

3,246

1,957

Accrued clinical trial liabilities

23,701

21,729

Accrued compensation and benefits

8,255

8,943

Other accrued liabilities

8,882

8,423

Current portion of notes payable and bank obligations

3,164

4,870

Current portion of convertible loans

10,000

Current portion of restructuring

4,033

4,483

Deferred revenue

24,134

41,920

Total current liabilities

85,415

92,325

Long-term portion of notes payable and bank obligations

82,885

85,260

Long-term portion of convertible loans

239,244

91,385

Long-term portion of restructuring

6,456

9,495

Other long-term liabilities

7,768

7,844

Deferred revenue

16,321

Total liabilities

421,768

302,630

Commitments

Stockholders' equity:

Common stock, $0.001 par value; 400,000,000 shares authorized; issued and outstanding: 183,489,026 and 135,563,735 shares at September 30, 2012 and December 31, 2011, respectively:

183

135

Additional paid-in-capital

1,542,489

1,196,992

Accumulated other comprehensive income (loss)

(18)

(138)

Accumulated deficit

(1,201,809)

(1,106,357)

Total stockholders' equity

340,845

90,632

Total liabilities and stockholders' equity

$ 762,613

$ 393,262

[1]	The condensed consolidated balance sheet at December 31, 2011 has been derived from the audited consolidated financial statements at that date but does not include all of the information and footnotes required by U.S. generally accepted accounting principles for complete financial statements.

Condensed Consolidated Balance Sheets (Parenthetical) - $ / shares	Sep. 30, 2012	Dec. 31, 2011
Statement of Financial Position [Abstract]
Common stock, par value, in dollars per share	$ 0.001	$ 0.001
Common stock, shares authorized	400,000,000	200,000,000
Common stock, shares issued	183,489,026	135,563,735
Common stock, shares outstanding	183,489,026	135,563,735

Condensed Consolidated Statements Of Operations - USD ($) shares in Thousands, $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2012	Sep. 30, 2011	Sep. 30, 2012	Sep. 30, 2011
Revenues:
Contract	$ 9,301	$ 5,024	$ 16,934	$ 25,761
License	4,012	122,703	22,702	167,984
Collaboration reimbursement	0	545	0	2,583
Total revenues	13,313	128,272	39,636	196,328
Operating expenses:
Research and development	30,680	37,465	96,386	126,058
General and administrative	7,343	8,171	22,008	26,119
Restructuring charge	733	2,937	1,704	6,190
Total operating expenses	38,756	48,573	120,098	158,367
(Loss) income from operations	(25,443)	79,699	(80,462)	37,961
Other income (expense), net:
Interest income and other, net	318	98	818	1,479
Interest expense	(7,679)	(4,142)	(15,775)	(12,249)
Gain on sale of business	0	2,210	0	2,210
Total other income (expense), net	(7,361)	(1,834)	(14,957)	(8,560)
(Loss) income before income taxes	(32,804)	77,865	(95,419)	29,401
Income tax provision	(10)	0	(33)	0
Net (loss) income	$ (32,814)	$ 77,865	$ (95,452)	$ 29,401
Net (loss) income per share, basic, in dollars per share	$ (0.20)	$ 0.60	$ (0.63)	$ 0.24
Net (loss) income per share, diluted, in dollars per share	$ (0.20)	$ 0.59	$ (0.63)	$ 0.23
Shares used in computing basic (loss) income per share amounts	166,354	129,145	152,316	123,426
Shares used in computing diluted (loss) income per share amounts	166,354	131,344	152,316	129,430

Consolidated Statements Of Other Comprehensive Loss - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2012	Sep. 30, 2011	Sep. 30, 2012	Sep. 30, 2011
Statement of Other Comprehensive Income [Abstract]
Net (loss) income	$ (32,814)	$ 77,865	$ (95,452)	$ 29,401
Net unrealized (losses) gains on available-for-sale securities	(23)	(236)	120	(261)
Comprehensive (loss) income	$ (32,837)	$ 77,629	$ (95,332)	$ 29,140

- Definition

The change in equity [net assets] of a business enterprise during a period from transactions and other events and circumstances from non-owner sources which are attributable to the reporting entity. It includes all changes in equity during a period except those resulting from investments by owners and distributions to owners, but excludes any and all transactions which are directly or indirectly attributable to that ownership interest in subsidiary equity which is not attributable to the parent.

+ References + Details

- Definition

The portion of profit or loss for the period, net of income taxes, which is attributable to the parent.

+ References

Reference 1: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Glossary Net Income
-URI http://asc.fasb.org/extlink&oid=6518256

Reference 2: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 230
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-Section 45
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-URI http://asc.fasb.org/extlink&oid=6943989&loc=d3e3602-108585

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-URI http://asc.fasb.org/extlink&oid=6879464&loc=d3e573970-122913

Reference 4: http://www.xbrl.org/2003/role/presentationRef
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-Paragraph 1
-URI http://asc.fasb.org/extlink&oid=6371337&loc=d3e3550-109257

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-Section S99
-Paragraph 2
-Subparagraph (SX 210.5-03.18)
-URI http://asc.fasb.org/extlink&oid=6880815&loc=d3e20235-122688

Reference 6: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 944
-SubTopic 225
-Section S99
-Paragraph 1
-Subparagraph (SX 210.7-04.22)
-URI http://asc.fasb.org/extlink&oid=6879464&loc=d3e573970-122913

Reference 7: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Glossary Other Comprehensive Income
-URI http://asc.fasb.org/extlink&oid=6519514

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-Publisher FASB
-Name Accounting Standards Codification
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-URI http://asc.fasb.org/extlink&oid=20435746&loc=d3e565-108580

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-Publisher AICPA
-Name Accounting Research Bulletin (ARB)
-Number 51
-Paragraph 38
-Subparagraph d
-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

Reference 10: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Statement of Financial Accounting Standard (FAS)
-Number 130
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-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

Reference 11: http://www.xbrl.org/2003/role/presentationRef
-Publisher AICPA
-Name Accounting Research Bulletin (ARB)
-Number 51
-Paragraph A7
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Reference 12: http://www.xbrl.org/2003/role/presentationRef
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-Number 87-21
-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

Reference 13: http://www.xbrl.org/2003/role/presentationRef
-Publisher SEC
-Name Regulation S-X (SX)
-Number 210
-Section 03
-Paragraph 19
-Article 5

Reference 14: http://www.xbrl.org/2003/role/presentationRef
-Publisher AICPA
-Name Accounting Research Bulletin (ARB)
-Number 51
-Paragraph 38
-Subparagraph a
-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

Reference 15: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Statement of Financial Accounting Standard (FAS)
-Number 95
-Paragraph 28, 29, 30
-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

Reference 16: http://www.xbrl.org/2003/role/presentationRef
-Publisher SEC
-Name Regulation S-X (SX)
-Number 210
-Section 04
-Paragraph 20
-Article 9

+ Details

- Definition

Net of tax amount of unrealized holding gain (loss) before reclassification adjustments and transfers on available-for-sale securities.

+ References

Reference 1: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 220
-SubTopic 10
-Section 45
-Paragraph 10A
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-URI http://asc.fasb.org/extlink&oid=20435746&loc=SL7669646-108580

Reference 2: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
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-URI http://asc.fasb.org/extlink&oid=20435746&loc=d3e637-108580

Reference 3: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Statement of Financial Accounting Standard (FAS)
-Number 115
-Paragraph 13
-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

Reference 4: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Statement of Financial Accounting Standard (FAS)
-Number 130
-Paragraph 17, 22
-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

Reference 5: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Statement of Financial Accounting Standard (FAS)
-Number 130
-Paragraph 24
-Subparagraph b
-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

Reference 6: http://www.xbrl.org/2003/role/presentationRef
-Publisher AICPA
-Name Accounting Research Bulletin (ARB)
-Number 51
-Paragraph 38
-Subparagraph c(3)
-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

+ Details

Condensed Consolidated Statements Of Cash Flows - USD ($)
$ in Thousands

9 Months Ended

Sep. 30, 2012

Sep. 30, 2011

Cash flows from operating activities:

Net (loss) income

$ (95,452)

$ 29,401

Adjustments to reconcile net (loss) income to net cash used in operating activities:

Depreciation and amortization

4,071

5,035

Stock-based compensation expense

6,222

9,409

Restructuring (credit) charge for property and equipment

(141)

379

Gain on sale of business

(2,210)

Accretion of debt discount

8,624

5,900

Other

3,450

3,637

Changes in assets and liabilities:

Other receivables

27,082

1,242

Prepaid expenses and other current assets

(1,892)

(1,522)

Other assets

(1,983)

701

Accounts payable and other accrued expenses

3,280

(2,225)

Restructuring liability

(3,489)

(3,886)

Other long-term liabilities

(76)

(758)

Deferred revenue

(34,106)

(175,162)

Net cash used in operating activities

(84,410)

(130,059)

Cash flows from investing activities:

Purchases of property and equipment

(1,528)

(712)

Proceeds from sales of property and equipment

877

Proceeds on sale of business

3,010

(Increase) decrease in restricted cash and investments

(35,989)

2,200

Proceeds from maturities of marketable securities

236,323

117,244

Purchases of marketable securities

(359,524)

(210,580)

Net cash used in investing activities

(159,841)

(88,838)

Cash flows from financing activities:

Proceeds from issuance of common stock, net

203,479

179,377

Proceeds from convertible notes, net

277,673

Proceeds from exercise of stock options and warrants

901

11,705

Proceeds from employee stock purchase plan

828

987

Proceeds from note payable and bank obligations

2,589

Principal payments on notes payable and bank obligations

(4,082)

(6,990)

Net cash provided by financing activities

478,799

187,668

Net increase (decrease) in cash and cash equivalents

234,548

(31,229)

Cash and cash equivalents, at beginning of period

74,257

^[1]

97,440

Cash and cash equivalents, at end of period

$ 308,805

$ 66,211

[1]	The condensed consolidated balance sheet at December 31, 2011 has been derived from the audited consolidated financial statements at that date but does not include all of the information and footnotes required by U.S. generally accepted accounting principles for complete financial statements.

Organization and Summary of Significant Accounting Policies

9 Months Ended

Sep. 30, 2012

Organization, Consolidation and Presentation of Financial Statements [Abstract]

Organization And Summary Of Significant Accounting Policies

Organization and Summary of Significant Accounting Policies

Organization

Exelixis, Inc. (“Exelixis,” “we,” “our” or “us”) is a biotechnology company committed to developing small molecule therapies for the treatment of cancer. We are focusing our proprietary resources and development efforts exclusively on cabozantinib (formerly known as XL184), our most advanced product candidate, in order to maximize the therapeutic and commercial potential of this compound. We believe cabozantinib has the potential to be a high-quality, broadly active, differentiated pharmaceutical product that can make a meaningful difference in the lives of patients. We have also established a portfolio of other novel compounds that we believe have the potential to address serious unmet medical needs, many of which are being advanced by partners as part of collaborations.

Basis of Presentation

The accompanying unaudited condensed consolidated financial statements have been prepared in accordance with accounting principles generally accepted in the United States for interim financial information and pursuant to Form 10-Q and Article 10 of Regulation S-X of the Securities and Exchange Commission (“SEC”). Accordingly, they do not include all of the information and footnotes required by U.S. generally accepted accounting principles (“GAAP”) for complete financial statements. In our opinion, all adjustments (consisting of normal recurring adjustments) considered necessary for a fair presentation of the results of operations and cash flows for the period presented have been included.

Exelixis adopted a 52- or 53-week fiscal year that ends on the Friday closest to December 31^st. Fiscal year 2011, a 52-week year, ended on December 30, 2011, and fiscal year 2012, a 52-week year, will end on December 28, 2012. For convenience, references in this report as of and for the fiscal quarters ended September 30, 2011 and September 28, 2012, and as of the fiscal year ended December 30, 2011, are indicated as ended September 30, 2011 and 2012, and as ended December 31, 2011, respectively.

Operating results for the three and nine months ended September 30, 2012 are not necessarily indicative of the results that may be expected for the fiscal year ending December 31, 2012 or for any future period. These financial statements and notes should be read in conjunction with the consolidated financial statements and notes thereto for the fiscal year ended December 31, 2011 included in our Annual Report on Form 10-K filed with the SEC on February 22, 2012.

Basis of Consolidation

The consolidated financial statements include the accounts of Exelixis and those of our wholly-owned subsidiaries. All intercompany balances and transactions have been eliminated.

Use of Estimates

The preparation of the consolidated financial statements is in conformity with GAAP, which requires management to make estimates and assumptions that affect the reported amounts of assets, liabilities, revenue and expenses, and related disclosures. On an ongoing basis, management evaluates its estimates including, but not limited to, those related to revenue recognition, clinical trial accruals, restructuring and stock option valuation. We base our estimates on historical experience and on various other market-specific and other relevant assumptions that are believed to be reasonable under the circumstances, the results of which form the basis for making judgments about the carrying values of assets and liabilities that are not readily apparent from other sources. Actual results could differ materially from those estimates.

Cash and Investments

We consider all highly liquid investments purchased with an original maturity of three months or less to be cash equivalents. We invest in high-grade, short-term commercial paper and money market funds, which are subject to minimal credit and market risk.

Historically, all marketable securities were classified as available-for-sale, were carried at fair value and were viewed as available for use in current operations. Therefore, we had classified certain investments as short-term marketable securities, even though their stated maturity dates may have been one year or more beyond the balance sheet date. As of September 30, 2012, we continue to classify all marketable securities as available-for-sale; however, due to the increase in our cash balances as a result of the financing activities we conducted during the three months ended September 30, 2012, we no longer require these marketable securities for use in current operations, and have accordingly classified those securities that mature in more than 12 months as Long-term investments on our Condensed Consolidated Balance Sheets. Certain investments that collateralize loan balances that extend over 12 months have been classified as Long-term investments, in association with the loan arrangement; they are not restricted to withdrawal. Unrealized gains and losses on available-for-sale investments are reported as a separate component of stockholders’ equity. Realized gains and losses, net, and interest and dividends on available-for-sale securities are recorded in our Condensed Consolidated Statement of Operations as Interest income and other, net. The cost of securities sold is based on the specific identification method.

All our marketable securities are subject to quarterly reviews for impairment that is deemed to be other-than-temporary. An investment is considered other-than-temporarily impaired when its fair value is below its amortized cost and (1) we intend to sell the security, (2) it is “more likely than not” that we will be required to sell the security before recovery of its amortized cost basis or (3) the present value of expected cash flows from the investment is not expected to recover the entire amortized cost basis.

The following summarizes available-for-sale securities as of September 30, 2012 (in thousands):



	Amortized Cost		Gross Unrealized Gains		Gross Unrealized Losses			Fair Value
Money market funds	$	139,645	$	7	$	(4	)	$	139,648
Commercial paper	258,942		17		—			258,959
Corporate bonds	162,787		44		(94		)	162,737
U.S. Government sponsored enterprises	81,787		16		(2		)	81,801
Municipal bonds	31,566		—		(3		)	31,563
Total	$	674,727	$	84	$	(103	)	$	674,708
	Amortized Cost		Gross Unrealized Gains		Gross Unrealized Losses			Fair Value
As reported:
Cash and cash equivalents	$	308,804	$	1	$	—		$	308,805
Marketable securities	163,543		64		(66		)	163,541
Restricted cash and investments	40,185		7		(4		)	40,188
Long-term investments	162,195		12		(33		)	162,174
Total	$	674,727	$	84	$	(103	)	$	674,708

As of September 30, 2012, all securities that were in an unrealized loss position have been so for less than one year and the unrealized losses were due to market conditions and were not attributed to credit risk. Based on the scheduled maturities of our marketable securities, we concluded that the unrealized losses in our investment securities are not other-than-temporary, as it is more likely than not that we will hold these investments for a period of time sufficient for a recovery of our cost basis.

The following summarizes available-for-sale securities as of December 31, 2011 (in thousands):



	Amortized Cost		Gross Unrealized Gains		Gross Unrealized Losses			Fair Value
Money market funds	$	81,986	$	—	$	—		$	81,986
Commercial paper	29,079		2		(1		)	29,080
Corporate bonds	116,068		22		(169		)	115,921
U.S. Government sponsored enterprises	37,237		12		—			37,249
Municipal bonds	19,488		—		(3		)	19,485
Total	$	283,858	$	36	$	(173	)	$	283,721
	Amortized Cost		Gross Unrealized Gains		Gross Unrealized Losses			Fair Value
As reported:
Cash and cash equivalents	$	74,256	$	1	$	—		$	74,257
Marketable securities	120,143		35		(173		)	120,005
Restricted cash and investments	4,199		—		—			4,199
Long-term investments	85,260		—		—			85,260
Total	$	283,858	$	36	$	(173	)	$	283,721

The following summarizes available-for-sale securities as of September 30, 2012 by contractual maturity (in thousands):



	Amortized Cost		Gross Unrealized Gains		Gross Unrealized Losses			Fair Value
Mature in less than one year	$	555,899	$	65	$	(67	)	$	555,897
Mature in one to two years	118,828		19		(36		)	118,811
Total	$	674,727	$	84	$	(103	)	$	674,708

The following summarizes available-for-sale securities as of December 31, 2011 by contractual maturity (in thousands):



	Amortized Cost		Gross Unrealized Gains		Gross Unrealized Losses			Fair Value
Mature in less than one year	$	259,209	$	24	$	(151	)	$	259,082
Mature in one to two years	24,649		12		(22		)	24,639
Total	$	283,858	$	36	$	(173	)	$	283,721

Fair Value Measurements

The fair value of our financial instruments reflects the amounts that would be received upon sale of an asset or paid to transfer a liability in an orderly transaction between market participants at the measurement date (exit price). The fair value hierarchy has the following three levels:

Level 1—quoted prices in active markets for identical assets and liabilities.

Level 2—observable inputs other than quoted prices in active markets for identical assets and liabilities.

Level 3—unobservable inputs.

Our Level 1 investments and liabilities are valued using quoted prices in active markets or based upon other observable inputs. Our Level 2 inputs were determined using prices from independent pricing services based on quoted prices in active markets for similar instruments or on industry models using data inputs, such as interest rates and prices that can be directly observed or corroborated in active markets. There were no transfers between Level 1 and Level 2 of the fair value hierarchy, as determined at the end of each reporting period. The following table sets forth the fair value of our financial assets that were measured on a recurring basis as of September 30, 2012 and December 31, 2011, respectively (in thousands):

As of September 30, 2012:



	Level 1		Level 2		Level 3		Total
Money market funds	$	139,648	$	—	$	—	$	139,648
Commercial paper	—		258,959		—		258,959
Corporate bonds	—		162,737		—		162,737
U.S. Government sponsored agencies	—		81,801		—		81,801
Municipal bonds	—		31,563		—		31,563
Total	$	139,648	$	535,060	$	—	$	674,708

As of December 31, 2011:



	Level 1		Level 2		Level 3		Total
Money market funds	$	81,986	$	—	$	—	$	81,986
Commercial paper	—		29,080		—		29,080
Corporate bonds	—		115,921		—		115,921
U.S. Government sponsored agencies	—		37,249		—		37,249
Municipal bonds	—		19,485		—		19,485
Total	$	81,986	$	201,735	$	—	$	283,721

Silicon Valley Bank loan and Deerfield facility

We have estimated the fair value of our long-term debt instruments, where possible, using the net present value of the payments discounted at an interest rate that is consistent with money-market rates that would have been earned on our non-interest-bearing compensating balances, which is a Level 2 input. However, due to the unique structure of our 2010 financing with entities affiliated with Deerfield Management Company L.P. (“Deerfield”) and the current non-liquid market in structured notes, there is no practicable method to determine the fair value of this instrument. The fair value of our debt will fluctuate with movements of interest rates, increasing in periods of declining rates of interest, and declining in periods of increasing rates of interest. See “Management's Discussion and Analysis of Financial Condition and Results of Operations—Certain Factors Important to Understanding Our Financial Condition and Results of Operations—Deerfield Facility” and “Management’s Discussion and Analysis of Financial Condition and Results of Operations—Liquidity and Capital Resources—Cash Requirements” for details on the structure and terms of our 2010 financing with Deerfield.

Convertible Senior Subordinated Notes due 2019

On August 14, 2012, we issued and sold $287.5 million aggregate principal amount of 4.25% convertible senior subordinated notes due 2019 (the "2019 Notes"). The fair value of the 2019 Notes at September 30, 2012 is based on the average trading prices, a level 1 input. The 2019 Notes are not marked-to-market and are shown at their original issuance value net of the unamortized discount; the portion of the value allocated to the conversion option is included in stockholders' equity in the accompanying unaudited Condensed Consolidated Balance Sheets at September 30, 2012. See Note 6 to the Condensed Consolidated Financial Statements for further information regarding the 2019 Notes.

The estimated fair value of our outstanding debt, excluding our 2010 financing with Deerfield, was as follows (in thousands):



	September 30, 2012		December 31, 2011
Equipment lines of credit	$	6,006	$	10,066
Silicon Valley Bank loan	77,981		77,835
Convertible senior subordinated notes due 2019 (face value $287,500)	305,900		—
Total	$	389,887	$	87,901

Our payment commitments associated with these debt instruments are fixed during the corresponding terms and comprise interest payments, principal payments or a combination thereof.

Long-Lived Assets

The carrying value of our long-lived assets is reviewed for impairment whenever events or changes in circumstances indicate that the asset may not be recoverable. An impairment loss would be recognized when estimated future cash flows expected to result from the use of the asset and its eventual disposition are less than its carrying amount. Long-lived assets include property and equipment and identified intangible assets. In the nine months ended September 30, 2011, we recorded impairment charges associated with our property and equipment in the amount of approximately $0.3 million in connection with our 2010 and 2011 restructurings. The charges related to the 2010, 2011 and 2012 restructurings (collectively, the "Restructurings") recorded during the nine months ended September 30, 2012 were $0.3 million. See Note 4 to the Condensed Consolidated Financial Statements for further information on the restructurings.

Concentration of Credit Risk

Financial instruments that potentially subject us to concentrations of credit risk are primarily cash and cash equivalents, accounts receivable and investments in marketable securities. Cash equivalents and marketable securities consist of money market funds, taxable commercial paper, corporate bonds with high credit quality, obligations of U.S. government sponsored enterprises and municipal bonds. All cash and cash equivalents and marketable securities are maintained with financial institutions that management believes are creditworthy. Other receivables are typically unsecured and are concentrated in the pharmaceutical and biotechnology industries. Accordingly, we may be exposed to credit risk generally associated with pharmaceutical and biotechnology companies. We have incurred no bad debt expense since inception.

Net (Loss) income Per Share

Basic net (loss) income per share is computed by dividing net (loss) income for the period by the weighted average number of shares of common stock outstanding during the period. Diluted net (loss) income per share gives effect to potential incremental common shares issuable (1) upon the exercise of stock options and warrants, (2) in connection with vesting of restricted stock units (“RSUs”), (3) pursuant to our employee stock purchase plan, and (4) upon conversion of our loan with GlaxoSmithKline, which was fully repaid in October 2011, and of the 2019 Notes (both of which were calculated using an as-if-converted method).

The following table sets forth a reconciliation of basic and diluted net (loss) income per share (in thousands, except per share amounts):



	Three Months Ended September 30,		Nine Months Ended September 30,
	2012	2011	2012	2011
Numerator:
Net (loss) income	$(32,814)	$77,865	$(95,452)	$29,401
Denominator:
Shares used in computing basic (loss) income per share amounts	166,354	129,145	152,316	123,426
Add effect of dilutive securities:
Shares issuable upon conversion of our GlaxoSmithKline loan	—	449	—	1,568
Shares issuable upon the exercise of outstanding stock options	—	1,444	—	3,471
Shares issuable pursuant to the issuance of vested RSUs	—	144	—	558
Shares issuable pursuant to the exercise of warrants	—	48	—	281
Shares issuable upon the purchase of ESPP	—	114	—	126
Shares used in computing diluted net (loss) income per common share	—	2,199	—	6,004
Shares used in computing diluted (loss) income per share amounts	166,354	131,344	152,316	129,430
Net (loss) income per share, basic	$(0.20)	$0.60	$(0.63)	$0.24
Net (loss) income per share, diluted	$(0.20)	$0.59	$(0.63)	$0.23

For the three and nine months ended September 30, 2012, 71.9 million total potential common shares were excluded from the total number of dilutive shares because their effect is antidilutive. Of these excluded shares, 54.1 million potential common shares related to the 2019 Notes and the remaining 17.7 million potential common shares related to RSUs, common stock options, our employee stock purchase plan and warrants. The total number of antidilutive outstanding potential common shares excluded from the net income per share computation of RSUs, common stock options, warrants and shares related to our GlaxoSmithKline convertible debt were 15.5 million and 7.4 million for the three and nine months ended September 30, 2011, respectively.

Collaboration Arrangements

Collaborative agreement reimbursement revenues or collaboration cost-sharing expenses are recorded as earned or owed based on the performance requirements by both parties under the respective contracts. There were no such reimbursements for the three and nine months ended September 30, 2012, and we do not expect to record any further collaboration reimbursement revenues under our current collaborations.

Foreign Currency Translation and Remeasurement

Assets and liabilities denominated in currencies other than the functional currency are remeasured using exchange rates in effect at the end of the period and related gains or losses are recorded in Interest income and other, net. Gains and losses on the remeasurement of foreign currency assets and liabilities were not material for the periods presented.

Recently Adopted Accounting Pronouncements

In December 2011, Accounting Standards Codification Topic 350, Testing Goodwill for Impairment was amended to allow the option of performing a qualitative assessment in evaluating goodwill for impairment. We adopted this guidance beginning January 1, 2012, and it did not have a material effect on our consolidated financial statements.

In May 2011, Accounting Standards Codification Topic 820, Fair Value Measurement was amended to converge U.S. and international accounting standards and provide more detailed disclosure. We adopted this guidance beginning January 1, 2012 and added additional disclosure as required. The amendment did not have a material effect on our consolidated financial statements.

Recently Issued Accounting Pronouncements

In December 2011, Accounting Standards Codification Topic 210, Balance Sheet was amended to converge U.S. and international accounting standards, and requires additional disclosure about offsetting of financial instruments. This guidance will be effective January 1, 2013 and we are evaluating the effect on our consolidated financial statements.

Stock-Based Compensation

9 Months Ended

Sep. 30, 2012

Share-based Compensation [Abstract]

Stock-Based Compensation

We recorded and allocated employee stock-based compensation expenses as follows (in thousands):



	Three Months Ended September 30,				Nine Months Ended September 30,
	2012		2011		2012		2011
Research and development expense	$	970	$	1,378	$	3,202	$	4,557
General and administrative expense	923		1,401		2,970		4,102
Restructuring-related stock-based compensation expense	—		176		—		625
Total employee stock-based compensation expense	$	1,893	$	2,955	$	6,172	$	9,284

We use the Black-Scholes option pricing model to value our stock options. The expected life computation is based on historical exercise patterns and post-vesting termination behavior. We considered implied volatility as well as our historical volatility in developing our estimate of expected volatility. The fair value of employee share-based payments awards was estimated using the following assumptions and weighted average fair values:



	Stock Options Three Months Ended September 30,						Employee Stock Purchase Plan Three Months Ended September 30,
	2012			2011			2012			2011
Weighted average grant date fair value	$	3.31		$	3.28		$	1.63		$	4.24
Risk-free interest rate	0.81		%	0.97		%	0.15		%	0.10		%
Dividend yield	0		%	0		%	0		%	0		%
Volatility	69		%	70		%	68		%	70		%
Expected life	5.6 years			5.4 years			0.5 years			0.5 years

	Stock Options Nine Months Ended September 30,						Employee Stock Purchase Plan Nine Months Ended September 30,
	2012			2011			2012			2011
Weighted average grant date fair value	$	3.27		$	3.52		$	2.13		$	3.05
Risk-free interest rate	0.82		%	1.05		%	0.10		%	0.13		%
Dividend yield	0		%	0		%	0		%	0		%
Volatility	69		%	70		%	68		%	68		%
Expected life	5.7 years			5.5 years			0.5 years			0.5 years

A summary of all stock option activity for the nine months ended September 30, 2012 is presented below:



	Shares		Weighted Average Exercise Price		Weighted Average Remaining Contractual Term	Aggregate Intrinsic Value
Options outstanding at December 31, 2011	17,436,378		$	7.16
Granted	3,300,546		5.49
Exercised	(175,708	)	5.12
Cancelled	(1,399,526	)	7.92
Options outstanding at September 30, 2012	19,161,690		$	6.84	4.64 years	$	287,800
Exercisable at September 30, 2012	13,559,920		$	7.32	3.80 years	$	239,408

As of September 30, 2012, $16.0 million of total unrecognized compensation expense related to employee stock options was expected to be recognized over a weighted-average period of 3.09 years.

A summary of all RSU activity for the nine months ended September 30, 2012 is presented below:



	Shares		Weighted Average Grant Date Fair Value		Weighted Average Remaining Contractual Term	Aggregate Intrinsic Value
RSUs outstanding at December 31, 2011	1,391,691		$	6.92
Awarded	711,575		5.53
Released	(459,416	)	7.33
Forfeited	(201,987	)	6.74
RSUs outstanding at September 30, 2012	1,441,863		$	6.13	1.84 years	$	6,956,995

As of September 30, 2012, $6.8 million of total unrecognized compensation expense related to employee RSUs was expected to be recognized over a weighted-average period of 3.06 years.

- Definition

The entire disclosure for compensation-related costs for equity-based compensation, which may include disclosure of policies, compensation plan details, allocation of equity compensation, incentive distributions, equity-based arrangements to obtain goods and services, deferred compensation arrangements, employee stock ownership plan details and employee stock purchase plan details.

+ References

Reference 1: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 505
-SubTopic 50
-Section 50
-Paragraph 1
-URI http://asc.fasb.org/extlink&oid=6406099&loc=d3e25284-112666

Reference 2: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 718
-SubTopic 40
-Section 50
-Paragraph 1
-URI http://asc.fasb.org/extlink&oid=6418621&loc=d3e17540-113929

Reference 3: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 718
-SubTopic 10
-Section 50
-Paragraph 2
-URI http://asc.fasb.org/extlink&oid=6415400&loc=d3e5070-113901

Reference 4: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 718
-SubTopic 10
-Section 50
-Paragraph 1
-URI http://asc.fasb.org/extlink&oid=6415400&loc=d3e5047-113901

Reference 5: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 718
-SubTopic 10
-Section 50
-Paragraph 4
-URI http://asc.fasb.org/extlink&oid=6415400&loc=d3e5444-113901

Reference 6: http://www.xbrl.org/2003/role/presentationRef
-Publisher SEC
-Name Staff Accounting Bulletin (SAB)
-Number Topic 14

Reference 7: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Statement of Financial Accounting Standard (FAS)
-Number 123R
-Paragraph 64, 65, A240
-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

Reference 8: http://www.xbrl.org/2003/role/presentationRef
-Publisher AICPA
-Name Statement of Position (SOP)
-Number 93-6
-Paragraph 53
-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

+ Details

Collaborations	9 Months Ended
Collaborations	Sep. 30, 2012
Collaborations [Abstract]
Collaborations	Collaborations Merck On December 21, 2011, we entered into an agreement with Merck & Co., Inc., known as MSD outside of the United States and Canada (“Merck”), pursuant to which we granted to Merck an exclusive worldwide license to our phosphoinositide-3 kinase delta (“PI3K-delta”) program, including XL499 and other related compounds. Pursuant to the terms of the agreement, Merck will have sole responsibility to research, develop, and commercialize compounds from our PI3K-delta program. As a result we recognized $1.3 million in revenue in December 2011. Merck was required to pay us an up-front cash payment of $12.0 million in connection with the agreement, which we received on January 19, 2012. Under the terms of the agreement, we completed the transfer of the license and associated knowledge within ninety days of the effective date of the agreement and accordingly recognized the remaining unrecognized up-front payment of $10.7 million during the three months ended March 31, 2012. We will be eligible to receive potential development and regulatory milestone payments for multiple indications of up to $239.0 million. We will also be eligible to receive combined sales performance milestones of up to $375.0 million and royalties on net sales of products emerging from the agreement. Milestones and royalties are payable on compounds emerging from our PI3K-delta program or from certain compounds that arise from Merck’s internal discovery efforts targeting PI3K-delta during a certain period. Merck may at any time, upon specified prior notice to us, terminate the license. In addition, either of us may terminate the agreement for the other party’s uncured material breach. In the event of termination by Merck at will or by us for Merck’s uncured material breach, the license granted to Merck would terminate. In the event of a termination by us for Merck’s uncured material breach, we would receive a royalty-free license from Merck to develop and commercialize certain joint products. In the event of termination by Merck for our uncured material breach, Merck would retain the licenses from us, and we would receive reduced royalties from Merck on commercial sales of products. Bristol-Myers Squibb Company 2007 Cancer Collaboration In December 2006, we entered into a worldwide collaboration with Bristol-Myers Squibb Company (“Bristol-Myers Squibb”), which became effective in January 2007, to discover, develop and commercialize novel targeted therapies for the treatment of cancer. We were responsible for discovery and preclinical development of small molecule drug candidates directed against mutually selected targets. In January 2007, Bristol-Myers Squibb made an up-front payment of $60.0 million to us for which we granted Bristol-Myers Squibb the right to select up to three investigational new drug (“IND”) candidates from six future Exelixis compounds. We recognized the up-front payment as revenues over the estimated research term. For each IND candidate selected, we were entitled to receive a $20.0 million selection milestone from Bristol-Myers Squibb. Once selected, Bristol-Myers Squibb became responsible for leading the further development and commercialization of the selected IND candidates. In addition, we had the right to opt in to co-promote the selected IND candidates, in which case we would equally share all development costs and profits in the United States. In January 2008 and November 2008, Bristol-Myers Squibb exercised its option under the collaboration to develop and commercialize XL139 (BMS-833923), a Hedgehog inhibitor, and XL413 (BMS-863233), a CDC7 inhibitor, respectively. Under the terms of the collaboration agreement, the selection of XL139 and XL413 by Bristol-Myers Squibb entitled us to milestone payments of $20.0 million each, which we received in February 2008 and December 2008, respectively. In addition, we exercised our option under the collaboration agreement to co-develop and co-commercialize each of XL139 and XL413 in the United States. In September 2010, we and Bristol-Myers Squibb terminated the XL413 program due to an unfavorable pharmacological profile observed in phase 1 clinical evaluation. Additionally, in connection with an amendment to the collaboration, which became effective in November 2010, we exercised our right to opt-out of further co-development of XL139 in consideration for a payment of $20.0 million. This opt-out payment and the remaining deferred revenue balance as of the effective date of the opt-out, November 2010, were combined with and recognized in conjunction with the up-front fees received related to our TGR5 license agreement and ROR collaboration agreement entered into with Bristol-Myers Squibb in 2010, and will be recognized over the agreement with the longest term. Please refer to “2010 Collaboration Agreements” within this note. The collaboration agreement was amended and restated in April 2011 in connection with an assignment of patents to one of our wholly-owned subsidiaries. We have no further responsibility for conducting new activities or funding new development or commercialization activities with respect to XL139 and will therefore no longer be eligible to share profits on sales of any commercialized products under the collaboration. We will continue to be eligible to receive regulatory and commercial milestones as well as double-digit royalties on any future sales of any products commercialized under the collaboration. As a result of the November 2010 amendment to the collaboration, the research term has ended, and we have no further obligation to deliver to Bristol-Myers Squibb a third IND candidate under the collaboration. 2010 Collaboration Agreements TGR5 License Agreement In October 2010, we entered into a global license agreement with Bristol-Myers Squibb for XL475 (and any potential backups), a preclinical compound that modulates the metabolic target known as TGR5 (the “TGR5 License Agreement”). Pursuant to the terms of the TGR5 License Agreement, Bristol-Myers Squibb received a worldwide exclusive license to XL475 and has sole control and responsibility for all subsequent research, development, commercial and manufacturing activities. The TGR5 License Agreement became effective in November 2010 following clearance under the Hart-Scott-Rodino Antitrust Improvement Act of 1976, as amended. The license agreement was amended and restated in April 2011 in connection with an assignment of patents to one of our wholly-owned subsidiaries. Under the license agreement, Bristol-Myers Squibb received a worldwide exclusive license to XL475 and sole control and responsibility for all research, development, commercial and manufacturing activities. In November 2010 we received a nonrefundable up-front cash payment of $35.0 million from Bristol-Myers Squibb. Additionally, for each product developed by Bristol-Myers Squibb under the license, we will be eligible to receive development and regulatory milestones of up to $250.0 million and commercial milestones of up to $150.0 million, as well as royalties on commercial sales of any such products. As of September 30, 2012, we have recognized aggregate license revenue of $24.1 million under this agreement. ROR Collaboration Agreement In October 2010, we entered into a worldwide collaboration with Bristol-Myers Squibb pursuant to which each party granted to the other certain intellectual property licenses to enable the parties to discover, optimize and characterize ROR antagonists that may subsequently be developed and commercialized by Bristol-Myers Squibb. In November 2010, we received a nonrefundable up-front cash payment of $5.0 million from Bristol-Myers Squibb. Additionally, for each product developed by Bristol-Myers Squibb under the collaboration, we will be eligible to receive development and regulatory milestones of up to $255.0 million and commercial milestones of up to $150.0 million, as well as royalties on commercial sales of any such products. The collaboration agreement was amended and restated in April 2011 in connection with an assignment of patents to one of our wholly-owned subsidiaries. In July 2011, we achieved a development preclinical milestone of $2.5 million. As of September 30, 2012, we have recognized aggregate license revenue of $5.3 million under this agreement.

Restructurings

9 Months Ended

Sep. 30, 2012

Restructuring Charges [Abstract]

Restructurings

During 2010, we implemented two restructurings that resulted in an overall reduction in our workforce of 386 employees. As a consequence of our decision to focus our proprietary resources and development efforts on the development and commercialization of cabozantinib, we implemented additional restructurings in both March 2011 and May 2012, resulting in further reductions to our workforce. The aggregate reduction in headcount from the Restructurings is 422 employees.

We have recorded aggregate restructuring charges of $44.6 million in connection with the Restructurings, of which $21.3 million related to termination benefits and $23.3 million related to facility charges and the impairment of various assets. For the nine months ended September 30, 2012 and 2011, we recorded restructuring charges of approximately $1.7 million and $6.2 million, respectively. The charge for the nine months ended September 30, 2012, was primarily related to termination benefits and facility related charges in connection with the exit of all or portions of three of our South San Francisco buildings. The total outstanding restructuring liability related to the Restructurings is included in current and long-term portion of restructuring on our Condensed Consolidated Balance Sheets.

As of September 30, 2012, the components of these liabilities are summarized in the following table (in thousands):



	Employee Severance And Other Benefits			Facility Charges			Asset Impairment, net of sales			Legal and Other Fees			Total
Ending accrual balance as of December 31, 2011	$	6		$	13,921		$	—		$	51		$	13,978
Restructuring charge (credit)	1,046			866			(180		)	(28		)	1,704
Cash payments	(909		)	(4,451		)	—			(3		)	(5,363		)
Adjustments or non-cash credits	(10		)	—			(697		)	—			(707		)
Proceeds from sale of assets	—			—			877			—			877
Ending accrual balance as of September 30, 2012	$	133		$	10,336		$	—		$	20		$	10,489

We expect to incur additional restructuring charges of approximately $1.3 million, primarily related to the exit of all or portions of three of our South San Francisco buildings and will be recorded through the end of the building lease terms, the last of which ends in 2017.

- Definition

The entire disclosure for restructuring and related activities. Description of restructuring activities such as exit and disposal activities, include facts and circumstances leading to the plan, the expected plan completion date, the major types of costs associated with the plan activities, total expected costs, the accrual balance at the end of the period, and the periods over which the remaining accrual will be settled.

+ References + Details

Sale of Shares of Common Stock	9 Months Ended
Sale of Shares of Common Stock	Sep. 30, 2012
Equity [Abstract]
Sale of Shares of Common Stock	Sales of Shares of Common Stock In March 2011, we completed a public offering of 17.3 million shares of our common stock pursuant to a shelf registration statement previously filed with the SEC, which the SEC declared effective on May 8, 2009. We received approximately $179.3 million in net proceeds from the offering after deducting the underwriting discount and related offering expenses. In February 2012, we completed a public offering of 12.7 million shares of our common stock pursuant to a shelf registration statement previously filed with the SEC, which the SEC declared effective on May 8, 2009. We received approximately $65 million in net proceeds from the offering after deducting the underwriting discount and related offering expenses.

- Definition

The entire disclosure for shareholders' equity, comprised of portions attributable to the parent entity and noncontrolling interest, if any, including other comprehensive income (as applicable). Including, but not limited to: (1) balances of common stock, preferred stock, additional paid-in capital, other capital and retained earnings; (2) accumulated balance for each classification of other comprehensive income and total amount of comprehensive income; (3) amount and nature of changes in separate accounts, including the number of shares authorized and outstanding, number of shares issued upon exercise and conversion, and for other comprehensive income, the adjustments for reclassifications to net income; (4) rights and privileges of each class of stock authorized; (5) basis of treasury stock, if other than cost, and amounts paid and accounting treatment for treasury stock purchased significantly in excess of market; (6) dividends paid or payable per share and in the aggregate for each class of stock for each period presented; (7) dividend restrictions and accumulated preferred dividends in arrears (in aggregate and per share amount); (8) retained earnings appropriations or restrictions, such as dividend restrictions; (9) impact of change in accounting principle, initial adoption of new accounting principle and correction of an error in previously issued financial statements; (10) shares held in trust for Employee Stock Ownership Plan (ESOP); (11) deferred compensation related to issuance of capital stock; (12) note received for issuance of stock; (13) unamortized discount on shares; (14) description, terms, and number of warrants or rights outstanding; (15) shares under subscription and subscription receivables, effective date of new retained earnings after quasi-reorganization and deficit eliminated by quasi-reorganization and, for a period of at least ten years after the effective date, the point in time from which the new retained dates; and (16) retroactive effective of subsequent change in capital structure.

+ References

Reference 1: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 235
-SubTopic 10
-Section S99
-Paragraph 1
-Subparagraph (SX 210.4-08.(d),(e))
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Reference 2: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 505
-SubTopic 10
-Section 50
-Paragraph 4
-URI http://asc.fasb.org/extlink&oid=6928386&loc=d3e21484-112644

Reference 3: http://www.xbrl.org/2003/role/presentationRef
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-Paragraph 2
-Subparagraph (SAB TOPIC 4.E)
-URI http://asc.fasb.org/extlink&oid=6228006&loc=d3e74512-122707

Reference 4: http://www.xbrl.org/2003/role/presentationRef
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-Name Accounting Standards Codification
-Topic 505
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Reference 5: http://www.xbrl.org/2003/role/presentationRef
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-Name Accounting Standards Codification
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-Paragraph 1
-Subparagraph (SX 210.5-02.29-31)
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-Name Accounting Standards Codification
-Topic 505
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-Paragraph 4
-Subparagraph (SAB TOPIC 4.C)
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Reference 7: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 505
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-Section 50
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-URI http://asc.fasb.org/extlink&oid=6928386&loc=d3e21506-112644

Reference 8: http://www.xbrl.org/2003/role/presentationRef
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-Name Accounting Standards Codification
-Topic 505
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-Section S99
-Paragraph 1
-Subparagraph (SX 210.3-04)
-URI http://asc.fasb.org/extlink&oid=6959260&loc=d3e187085-122770

Reference 9: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
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-Paragraph 2
-URI http://asc.fasb.org/extlink&oid=6405834&loc=d3e23285-112656

Reference 10: http://www.xbrl.org/2003/role/presentationRef
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-Name Accounting Standards Codification
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Reference 11: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Glossary Preferred Stock
-URI http://asc.fasb.org/extlink&oid=6521494

Reference 12: http://www.xbrl.org/2003/role/presentationRef
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-Name Accounting Standards Codification
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-URI http://asc.fasb.org/extlink&oid=6928386&loc=d3e21564-112644

Reference 14: http://www.xbrl.org/2003/role/presentationRef
-Publisher AICPA
-Name Accounting Research Bulletin (ARB)
-Number 43
-Section B
-Paragraph 7, 11A
-Chapter 1
-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

Reference 15: http://www.xbrl.org/2003/role/presentationRef
-Publisher AICPA
-Name Accounting Principles Board Opinion (APB)
-Number 12
-Paragraph 10
-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

Reference 16: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Statement of Financial Accounting Standard (FAS)
-Number 5
-Paragraph 15
-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

Reference 17: http://www.xbrl.org/2003/role/presentationRef
-Publisher SEC
-Name Regulation S-X (SX)
-Number 210
-Section 08
-Paragraph d
-Article 4

Reference 18: http://www.xbrl.org/2003/role/presentationRef
-Publisher SEC
-Name Regulation S-X (SX)
-Number 210
-Section 02
-Paragraph 29, 30, 31
-Article 5

Reference 19: http://www.xbrl.org/2003/role/presentationRef
-Publisher SEC
-Name Staff Accounting Bulletin (SAB)
-Number Topic 4
-Section E

Reference 20: http://www.xbrl.org/2003/role/presentationRef
-Publisher SEC
-Name Regulation S-X (SX)
-Number 210
-Section 08
-Article 4

Reference 21: http://www.xbrl.org/2003/role/presentationRef
-Publisher SEC
-Name Staff Accounting Bulletin (SAB)
-Number Topic 4
-Section C

Reference 22: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Statement of Financial Accounting Standard (FAS)
-Number 129
-Paragraph 2, 3, 4, 5, 6, 7, 8
-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

Reference 23: http://www.xbrl.org/2003/role/presentationRef
-Publisher SEC
-Name Regulation S-X (SX)
-Number 210
-Section 04
-Article 3

+ Details

Concurrent Debt and Equity Offerings

9 Months Ended

Sep. 30, 2012

Debt and Equity Offerings [Abstract]

Concurrent Debt and Equity Offerings

On August 14, 2012, we completed concurrent registered underwritten public offerings in which we sold $287.5 million aggregate principal amount of the 2019 Notes and 34.5 million shares of common stock at a price of $4.25 per share, generating aggregate net proceeds of $416.1 million.

The convertible debt offering resulted in net proceeds of $277.7 million after deducting the underwriting discount and offering expenses of $9.3 million and $0.5 million, respectively. The equity offering resulted in net proceeds of $138.4 million after deducting the underwriting discount of $7.7 million and other expenses of $0.5 million.

The 2019 Notes were issued pursuant to an indenture, as supplemented by a supplemental indenture with Wells Fargo Bank, National Association, as trustee (the "Trustee"), and mature on August 15, 2019, unless earlier converted, redeemed or repurchased. The 2019 Notes bear interest at the rate of 4.25% per annum, payable semi-annually in arrears on February 15 and August 15 of each year, beginning February 15, 2013. Subject to certain terms and conditions, at any time on or after August 15, 2016, we may redeem for cash all or a portion of the 2019 Notes. The redemption price will equal 100% of the principal amount of the 2019 Notes to be redeemed, plus accrued and unpaid interest, if any, to, but excluding, the redemption date.

Upon the occurrence of certain circumstances, holders may convert their 2019 Notes prior to the close of business on the business day immediately preceding May 15, 2019. On or after May 15, 2019, until the close of business on the second trading day immediately preceding August 15, 2019, holders may surrender their 2019 Notes for conversion at any time. Upon conversion, we will pay or deliver, as the case may be, cash, shares of our common stock or a combination of cash and shares of our common stock, at our election. The initial conversion rate of 188.2353 shares of common stock per $1,000 principal amount of 2019 Notes is equivalent to a conversion price of approximately $5.31 per share of common stock. The conversion rate is subject to adjustment upon the occurrence of certain events.

In connection with the convertible debt offering, $36.5 million of the proceeds were deposited into an escrow account which contains an amount of permitted securities sufficient to fund, when due, the total aggregate amount of the first six scheduled semi-annual interest payments on the 2019 Notes. The amount held in the escrow account is classified on our Condensed Consolidated Balance Sheets as Short-term restricted cash and investments and Restricted cash and investments of $12.2 million and $24.3 million, respectively, as of September 30, 2012. We have pledged our interest in the escrow account to the Trustee as security for our obligations under the 2019 Notes.

The 2019 Notes are accounted for in accordance with ASC Subtopic 470-20, Debt with Conversion and Other Options. Under ASC Subtopic 470-20, issuers of certain convertible debt instruments that have a net settlement feature and may be settled in cash upon conversion, including partial cash settlement, are required to separately account for the liability (debt) and equity (conversion option) components of the instrument. The carrying amount of the liability component of any outstanding debt instrument is computed by estimating the fair value of a similar liability without the conversion option. The amount of the equity component is then calculated by deducting the fair value of the liability component from the principal amount of the convertible debt instrument. The effective interest rate used in determining the liability component of the 2019 Notes was approximately 10%. This resulted in initial recognition of $149.2 million as the liability component and the residual $138.3 million as the debt discount with a corresponding increase to paid-in capital, the equity component, for the 2019 Notes. The underwriting discount of $9.3 million and offering expenses of $0.5 million were allocated between debt issuance costs and equity issuance costs in proportion to the allocation of the proceeds. Debt issuance costs of $5.1 million are included in Other long term assets on our Condensed Consolidated Balance Sheets as of September 30, 2012. Equity issuance costs of $4.7 million related to the convertible debt offering were recorded as an offset to additional paid-in capital.

The following is a summary of the liability component of the 2019 Notes as of September 30, 2012 (in thousands):



	September 30, 2012
Net carrying amount of the liability component	$	151,024
Unamortized discount of the liability component	$	136,476
Face Value of the 2019 Notes	$	287,500

The debt discount and debt issuance costs are amortized as interest expense through August 2019. For the three and nine months ended September 30, 2012, total interest expense related to the 2019 Notes was $3.2 million, relating to the 4.25% stated coupon rate and the amortization of the debt discount and debt issuance costs. The non-cash expense relating to the amortization of the debt discount for the three and nine months ended September 30, 2012 was $1.8 million.

Deerfield Financing	9 Months Ended
Deerfield Financing	Sep. 30, 2012
Debt Disclosure [Abstract]
Deerfield Financing	Deerfield Financing On June 2, 2010, we entered into a note purchase agreement with Deerfield, pursuant to which, on July 1, 2010, we sold to Deerfield an aggregate of $124.0 million initial principal amount of our secured convertible notes due June 2015 (the "Deerfield Notes") for an aggregate purchase price of $80.0 million, less closing fees and expenses of approximately $2.0 million. On August 6, 2012, the parties amended the note purchase agreement to permit the issuance of the 2019 Notes and modify certain optional prepayment rights. The amendment became effective upon the issuance of the 2019 Notes and the payment to Deerfield of a $1.5 million consent fee which is included in Other long term assets on our Condensed Consolidated Balance Sheets and will be amortized through June 2015, the remaining life of the Deerfield Notes. The outstanding principal amount of the Deerfield Notes bears interest in the annual amount of $6.0 million, payable quarterly in arrears. We will be required to make mandatory prepayments on the notes on an annual basis in 2013, 2014 and 2015 equal to 15% of certain revenues from our collaborative arrangements received during the prior fiscal year, subject to a maximum annual prepayment amount of $27.5 million and, for payments due in January 2013 and 2014, a minimum prepayment amount of $10.0 million. We may also prepay all or a portion (not less than $5.0 million) of the principal amount of the Deerfield Notes at an optional prepayment price based on a discounted principal amount (during the first three years of the term, subject to a prepayment premium) determined as of the date of prepayment, plus accrued and unpaid interest, plus in the case of a prepayment of the full principal amount of the Deerfield Notes (other than prepayments upon the occurrence of specified transactions relating to a change of control or a substantial sale of assets), all accrued interest that would have accrued between the date of such prepayment and the next anniversary of the note purchase agreement. Pursuant to the amendment of the note purchase agreement, any optional prepayment of the Deerfield Notes made on or prior to July 2, 3013 will be determined as if such prepayment occurred as of July 3, 2013. In lieu of making any optional or mandatory prepayment in cash, subject to certain limitations (including a cap on the number of shares issuable under the note purchase agreement), we have the right to convert all or a portion of the principal amount of the Deerfield Notes into, or satisfy all or any portion of the optional prepayment amounts or mandatory prepayment amounts (other than the first $10.0 million of mandatory prepayments required in 2013 and 2014 and any optional prepayments made prior to July 3, 2013) with shares of our common stock. Additionally, in lieu of making any payment of accrued and unpaid interest in respect of the Deerfield Notes in cash, subject to certain limitations, we may elect to satisfy any such payment with shares of our common stock. The number of shares of our common stock issuable upon conversion or in settlement of principal and interest obligations will be based upon the discounted trading price of our common stock over a specified trading period. Upon certain changes of control of our company, a sale or transfer of assets in one transaction or a series of related transactions for a purchase price of more than $400.0 million or a sale or transfer of more than 50% of our assets, Deerfield may require us to prepay the Deerfield Notes at the optional prepayment price, plus accrued and unpaid interest and any other accrued and reimbursable expenses (the “Put Price”). Upon an event of default, Deerfield may declare all or a portion of the Put Price to be immediately due and payable. We also entered into a security agreement in favor of Deerfield which provides that our obligations under the Deerfield Notes will be secured by substantially all of our assets except intellectual property. In connection with the amendment of the note purchase agreement, the security agreement was also amended to exclude any escrowed proceeds from the issuance of 2019 Notes from the collateral pledged to Deerfield. The note purchase agreement and the security agreement include customary representations and warranties and covenants made by us, including restrictions on the incurrence of additional indebtedness. The balance of unamortized closing fee and expenses of $1.1 million is included in Other long term assets on our Condensed Consolidated Balance Sheets. The carrying value of the loan as of September 30, 2012 is $98.2 million.

- Definition

The entire disclosure for information about short-term and long-term debt arrangements, which includes amounts of borrowings under each line of credit, note payable, commercial paper issue, bonds indenture, debenture issue, own-share lending arrangements and any other contractual agreement to repay funds, and about the underlying arrangements, rationale for a classification as long-term, including repayment terms, interest rates, collateral provided, restrictions on use of assets and activities, whether or not in compliance with debt covenants, and other matters important to users of the financial statements, such as the effects of refinancing and noncompliance with debt covenants.

+ References + Details

Income Taxes	9 Months Ended
Income Taxes	Sep. 30, 2012
Income Tax Disclosure [Abstract]
Income Taxes	Income Taxes We recorded an income tax provision of $0.01 million and $0.03 million for the three and nine months ended September 30, 2012, respectively, for tax-related interest associated with the audit by the Internal Revenue Service of our 2008, 2009 and 2010 tax years. During the three months ended September 30, 2012, we recognized a deferred tax liability of $54.4 million related to the 2019 Notes (see Note 6 of the Notes to our Consolidated Financial Statements for further discussion regarding the 2019 Notes). Under ASC 470-20 we are required to bifurcate our convertible debt instrument into two separate components: a liability component and an equity component, resulting in a basis difference between financial reporting and tax amounts associated with the liability component. This difference creates a temporary difference for purposes of applying ASC 740, Income Taxes. The deferred tax liability was primarily offset by a reduction in our tax valuation allowance. The resulting allocation of valuation allowance required a deferred tax liability of $0.4 million included in Other long-term liabilities and a deferred tax asset of $0.4 million in Prepaid expenses and other current assets in our Condensed Consolidated Balance Sheets as of September 30, 2012.

- Definition

The entire disclosure for income taxes. Disclosures may include net deferred tax liability or asset recognized in an enterprise's statement of financial position, net change during the year in the total valuation allowance, approximate tax effect of each type of temporary difference and carryforward that gives rise to a significant portion of deferred tax liabilities and deferred tax assets, utilization of a tax carryback, and tax uncertainties information.

+ References

+ Details

Organization and Summary of Significant Accounting Policies (Policy)

9 Months Ended

Sep. 30, 2012

Organization, Consolidation and Presentation of Financial Statements [Abstract]

Organization

Basis of Presentation

Fiscal Period, Policy

Exelixis adopted a 52- or 53-week fiscal year that ends on the Friday closest to December 31^st.

Basis of Consolidation

The consolidated financial statements include the accounts of Exelixis and those of our wholly-owned subsidiaries. All intercompany balances and transactions have been eliminated.

Use of Estimates

Cash and Investments

The following summarizes available-for-sale securities as of September 30, 2012 (in thousands):



	Amortized Cost		Gross Unrealized Gains		Gross Unrealized Losses			Fair Value
Money market funds	$	139,645	$	7	$	(4	)	$	139,648
Commercial paper	258,942		17		—			258,959
Corporate bonds	162,787		44		(94		)	162,737
U.S. Government sponsored enterprises	81,787		16		(2		)	81,801
Municipal bonds	31,566		—		(3		)	31,563
Total	$	674,727	$	84	$	(103	)	$	674,708
	Amortized Cost		Gross Unrealized Gains		Gross Unrealized Losses			Fair Value
As reported:
Cash and cash equivalents	$	308,804	$	1	$	—		$	308,805
Marketable securities	163,543		64		(66		)	163,541
Restricted cash and investments	40,185		7		(4		)	40,188
Long-term investments	162,195		12		(33		)	162,174
Total	$	674,727	$	84	$	(103	)	$	674,708

The following summarizes available-for-sale securities as of December 31, 2011 (in thousands):



	Amortized Cost		Gross Unrealized Gains		Gross Unrealized Losses			Fair Value
Money market funds	$	81,986	$	—	$	—		$	81,986
Commercial paper	29,079		2		(1		)	29,080
Corporate bonds	116,068		22		(169		)	115,921
U.S. Government sponsored enterprises	37,237		12		—			37,249
Municipal bonds	19,488		—		(3		)	19,485
Total	$	283,858	$	36	$	(173	)	$	283,721
	Amortized Cost		Gross Unrealized Gains		Gross Unrealized Losses			Fair Value
As reported:
Cash and cash equivalents	$	74,256	$	1	$	—		$	74,257
Marketable securities	120,143		35		(173		)	120,005
Restricted cash and investments	4,199		—		—			4,199
Long-term investments	85,260		—		—			85,260
Total	$	283,858	$	36	$	(173	)	$	283,721

The following summarizes available-for-sale securities as of September 30, 2012 by contractual maturity (in thousands):



	Amortized Cost		Gross Unrealized Gains		Gross Unrealized Losses			Fair Value
Mature in less than one year	$	555,899	$	65	$	(67	)	$	555,897
Mature in one to two years	118,828		19		(36		)	118,811
Total	$	674,727	$	84	$	(103	)	$	674,708

The following summarizes available-for-sale securities as of December 31, 2011 by contractual maturity (in thousands):



	Amortized Cost		Gross Unrealized Gains		Gross Unrealized Losses			Fair Value
Mature in less than one year	$	259,209	$	24	$	(151	)	$	259,082
Mature in one to two years	24,649		12		(22		)	24,639
Total	$	283,858	$	36	$	(173	)	$	283,721

Fair Value Measurements

Level 1—quoted prices in active markets for identical assets and liabilities.

Level 2—observable inputs other than quoted prices in active markets for identical assets and liabilities.

Level 3—unobservable inputs.

As of September 30, 2012:



	Level 1		Level 2		Level 3		Total
Money market funds	$	139,648	$	—	$	—	$	139,648
Commercial paper	—		258,959		—		258,959
Corporate bonds	—		162,737		—		162,737
U.S. Government sponsored agencies	—		81,801		—		81,801
Municipal bonds	—		31,563		—		31,563
Total	$	139,648	$	535,060	$	—	$	674,708

As of December 31, 2011:



	Level 1		Level 2		Level 3		Total
Money market funds	$	81,986	$	—	$	—	$	81,986
Commercial paper	—		29,080		—		29,080
Corporate bonds	—		115,921		—		115,921
U.S. Government sponsored agencies	—		37,249		—		37,249
Municipal bonds	—		19,485		—		19,485
Total	$	81,986	$	201,735	$	—	$	283,721

Silicon Valley Bank loan and Deerfield facility

Convertible Senior Subordinated Notes due 2019

The estimated fair value of our outstanding debt, excluding our 2010 financing with Deerfield, was as follows (in thousands):



	September 30, 2012		December 31, 2011
Equipment lines of credit	$	6,006	$	10,066
Silicon Valley Bank loan	77,981		77,835
Convertible senior subordinated notes due 2019 (face value $287,500)	305,900		—
Total	$	389,887	$	87,901

Our payment commitments associated with these debt instruments are fixed during the corresponding terms and comprise interest payments, principal payments or a combination thereof.

Long Lived Assets

Long-Lived Assets

Concentration of Credit Risk

Net Loss Per Share

Net (Loss) income Per Share

Collaboration Arrangements

Foreign Currency Translation and Remeasurement

Recently Adopted Accounting Pronouncements

Recently Issued Accounting Pronouncements

Organization and Summary of Significant Accounting Policies (Tables)

9 Months Ended

Sep. 30, 2012

Organization, Consolidation and Presentation of Financial Statements [Abstract]

Schedule of Available-for-Sale Securities

The following summarizes available-for-sale securities as of December 31, 2011 (in thousands):



	Amortized Cost		Gross Unrealized Gains		Gross Unrealized Losses			Fair Value
Money market funds	$	81,986	$	—	$	—		$	81,986
Commercial paper	29,079		2		(1		)	29,080
Corporate bonds	116,068		22		(169		)	115,921
U.S. Government sponsored enterprises	37,237		12		—			37,249
Municipal bonds	19,488		—		(3		)	19,485
Total	$	283,858	$	36	$	(173	)	$	283,721
	Amortized Cost		Gross Unrealized Gains		Gross Unrealized Losses			Fair Value
As reported:
Cash and cash equivalents	$	74,256	$	1	$	—		$	74,257
Marketable securities	120,143		35		(173		)	120,005
Restricted cash and investments	4,199		—		—			4,199
Long-term investments	85,260		—		—			85,260
Total	$	283,858	$	36	$	(173	)	$	283,721

The following summarizes available-for-sale securities as of September 30, 2012 (in thousands):



	Amortized Cost		Gross Unrealized Gains		Gross Unrealized Losses			Fair Value
Money market funds	$	139,645	$	7	$	(4	)	$	139,648
Commercial paper	258,942		17		—			258,959
Corporate bonds	162,787		44		(94		)	162,737
U.S. Government sponsored enterprises	81,787		16		(2		)	81,801
Municipal bonds	31,566		—		(3		)	31,563
Total	$	674,727	$	84	$	(103	)	$	674,708
	Amortized Cost		Gross Unrealized Gains		Gross Unrealized Losses			Fair Value
As reported:
Cash and cash equivalents	$	308,804	$	1	$	—		$	308,805
Marketable securities	163,543		64		(66		)	163,541
Restricted cash and investments	40,185		7		(4		)	40,188
Long-term investments	162,195		12		(33		)	162,174
Total	$	674,727	$	84	$	(103	)	$	674,708

Summary of Available-for-Sale Securities by Contractual Maturity

The following summarizes available-for-sale securities as of September 30, 2012 by contractual maturity (in thousands):



	Amortized Cost		Gross Unrealized Gains		Gross Unrealized Losses			Fair Value
Mature in less than one year	$	555,899	$	65	$	(67	)	$	555,897
Mature in one to two years	118,828		19		(36		)	118,811
Total	$	674,727	$	84	$	(103	)	$	674,708

The following summarizes available-for-sale securities as of December 31, 2011 by contractual maturity (in thousands):



	Amortized Cost		Gross Unrealized Gains		Gross Unrealized Losses			Fair Value
Mature in less than one year	$	259,209	$	24	$	(151	)	$	259,082
Mature in one to two years	24,649		12		(22		)	24,639
Total	$	283,858	$	36	$	(173	)	$	283,721

Schedule of Fair Value of Financial Assets Measured on a Recurring Basis

As of September 30, 2012:



	Level 1		Level 2		Level 3		Total
Money market funds	$	139,648	$	—	$	—	$	139,648
Commercial paper	—		258,959		—		258,959
Corporate bonds	—		162,737		—		162,737
U.S. Government sponsored agencies	—		81,801		—		81,801
Municipal bonds	—		31,563		—		31,563
Total	$	139,648	$	535,060	$	—	$	674,708

As of December 31, 2011:



	Level 1		Level 2		Level 3		Total
Money market funds	$	81,986	$	—	$	—	$	81,986
Commercial paper	—		29,080		—		29,080
Corporate bonds	—		115,921		—		115,921
U.S. Government sponsored agencies	—		37,249		—		37,249
Municipal bonds	—		19,485		—		19,485
Total	$	81,986	$	201,735	$	—	$	283,721

Schedule of Estimated Fair Value of Outstanding Debt

The estimated fair value of our outstanding debt, excluding our 2010 financing with Deerfield, was as follows (in thousands):



	September 30, 2012		December 31, 2011
Equipment lines of credit	$	6,006	$	10,066
Silicon Valley Bank loan	77,981		77,835
Convertible senior subordinated notes due 2019 (face value $287,500)	305,900		—
Total	$	389,887	$	87,901

Schedule of Potential Shares of Common Stock Excluded From Computation of Diluted Net Loss Per Share

The following table sets forth a reconciliation of basic and diluted net (loss) income per share (in thousands, except per share amounts):



	Three Months Ended September 30,		Nine Months Ended September 30,
	2012	2011	2012	2011
Numerator:
Net (loss) income	$(32,814)	$77,865	$(95,452)	$29,401
Denominator:
Shares used in computing basic (loss) income per share amounts	166,354	129,145	152,316	123,426
Add effect of dilutive securities:
Shares issuable upon conversion of our GlaxoSmithKline loan	—	449	—	1,568
Shares issuable upon the exercise of outstanding stock options	—	1,444	—	3,471
Shares issuable pursuant to the issuance of vested RSUs	—	144	—	558
Shares issuable pursuant to the exercise of warrants	—	48	—	281
Shares issuable upon the purchase of ESPP	—	114	—	126
Shares used in computing diluted net (loss) income per common share	—	2,199	—	6,004
Shares used in computing diluted (loss) income per share amounts	166,354	131,344	152,316	129,430
Net (loss) income per share, basic	$(0.20)	$0.60	$(0.63)	$0.24
Net (loss) income per share, diluted	$(0.20)	$0.59	$(0.63)	$0.23

- Definition

Tabular disclosure of available-for-sale securities which includes, but is not limited to, changes in the cost basis and fair value, fair value and gross unrealized gain (loss), fair values by type of security, contractual maturity and classification, amortized cost basis, contracts to acquire securities to be accounted for as available-for-sale, debt maturities, transfers to trading, change in net unrealized holding gain (loss) net of tax, continuous unrealized loss position fair value, aggregate losses qualitative disclosures, other than temporary impairment (OTTI) losses or other disclosures related to available for sale securities.

+ References

Reference 1: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 942
-SubTopic 320
-Section 50
-Paragraph 2
-URI http://asc.fasb.org/extlink&oid=6957658&loc=d3e62557-112803

Reference 2: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 320
-SubTopic 10
-Section 50
-Paragraph 7
-URI http://asc.fasb.org/extlink&oid=6872113&loc=d3e27337-111563

Reference 3: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
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Reference 4: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 942
-SubTopic 320
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-URI http://asc.fasb.org/extlink&oid=6957658&loc=d3e62586-112803

Reference 5: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 320
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-URI http://asc.fasb.org/extlink&oid=6872113&loc=d3e27161-111563

Reference 6: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
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-SubTopic 10
-Section 50
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-URI http://asc.fasb.org/extlink&oid=6872113&loc=d3e27357-111563

Reference 7: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
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-SubTopic 10
-Section 50
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-URI http://asc.fasb.org/extlink&oid=6872113&loc=d3e27290-111563

Reference 8: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Statement of Financial Accounting Standard (FAS)
-Number 115
-Paragraph 19, 20, 21
-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

Reference 9: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name FASB Staff Position (FSP)
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-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

Reference 10: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Emerging Issues Task Force (EITF)
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-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

+ Details

- Definition

Tabular disclosure of assets, including [financial] instruments measured at fair value that are classified in stockholders' equity, if any, by class that are measured at fair value on a recurring basis. The disclosures contemplated herein include the fair value measurements at the reporting date by the level within the fair value hierarchy in which the fair value measurements in their entirety fall, segregating fair value measurements using quoted prices in active markets for identical assets (Level 1), significant other observable inputs (Level 2), and significant unobservable inputs (Level 3).

+ References + Details

- Definition

Tabular disclosure of liabilities, including [financial] instruments measured at fair value that are classified in stockholders' equity, if any, by class that are measured at fair value on a recurring basis. The disclosures contemplated herein include the fair value measurements at the reporting date by the level within the fair value hierarchy in which the fair value measurements in their entirety fall, segregating fair value measurements using quoted prices in active markets for identical assets (Level 1), significant other observable inputs (Level 2), and significant unobservable inputs (Level 3). Where the quoted price in an active market for the identical liability is not available, the Level 1 input is the quoted price of an identical liability when traded as an asset.

+ References + Details

Stock-Based Compensation (Tables)

9 Months Ended

Sep. 30, 2012

Share-based Compensation [Abstract]

Schedule Of Allocated Employee Stock-Based Compensation Expenses

We recorded and allocated employee stock-based compensation expenses as follows (in thousands):



	Three Months Ended September 30,				Nine Months Ended September 30,
	2012		2011		2012		2011
Research and development expense	$	970	$	1,378	$	3,202	$	4,557
General and administrative expense	923		1,401		2,970		4,102
Restructuring-related stock-based compensation expense	—		176		—		625
Total employee stock-based compensation expense	$	1,893	$	2,955	$	6,172	$	9,284

Schedule Of Fair Value Of Employee Share-Based Payments Awards Estimated Using The Assumptions And Weighted Average Fair Values

The fair value of employee share-based payments awards was estimated using the following assumptions and weighted average fair values:



	Stock Options Three Months Ended September 30,						Employee Stock Purchase Plan Three Months Ended September 30,
	2012			2011			2012			2011
Weighted average grant date fair value	$	3.31		$	3.28		$	1.63		$	4.24
Risk-free interest rate	0.81		%	0.97		%	0.15		%	0.10		%
Dividend yield	0		%	0		%	0		%	0		%
Volatility	69		%	70		%	68		%	70		%
Expected life	5.6 years			5.4 years			0.5 years			0.5 years

	Stock Options Nine Months Ended September 30,						Employee Stock Purchase Plan Nine Months Ended September 30,
	2012			2011			2012			2011
Weighted average grant date fair value	$	3.27		$	3.52		$	2.13		$	3.05
Risk-free interest rate	0.82		%	1.05		%	0.10		%	0.13		%
Dividend yield	0		%	0		%	0		%	0		%
Volatility	69		%	70		%	68		%	68		%
Expected life	5.7 years			5.5 years			0.5 years			0.5 years

Summary Of All Stock Option Activity

A summary of all stock option activity for the nine months ended September 30, 2012 is presented below:



	Shares		Weighted Average Exercise Price		Weighted Average Remaining Contractual Term	Aggregate Intrinsic Value
Options outstanding at December 31, 2011	17,436,378		$	7.16
Granted	3,300,546		5.49
Exercised	(175,708	)	5.12
Cancelled	(1,399,526	)	7.92
Options outstanding at September 30, 2012	19,161,690		$	6.84	4.64 years	$	287,800
Exercisable at September 30, 2012	13,559,920		$	7.32	3.80 years	$	239,408

Summary Of All RSU Activity

A summary of all RSU activity for the nine months ended September 30, 2012 is presented below:



	Shares		Weighted Average Grant Date Fair Value		Weighted Average Remaining Contractual Term	Aggregate Intrinsic Value
RSUs outstanding at December 31, 2011	1,391,691		$	6.92
Awarded	711,575		5.53
Released	(459,416	)	7.33
Forfeited	(201,987	)	6.74
RSUs outstanding at September 30, 2012	1,441,863		$	6.13	1.84 years	$	6,956,995

- Definition

Tabular disclosure of the allocation of equity-based compensation costs to a given line item on the balance sheet and income statement for the period. This may include the reporting line for the costs and the amount capitalized and expensed.

+ References + Details

Restructurings (Tables)

9 Months Ended

Sep. 30, 2012

Restructuring Charges [Abstract]

Summary Of Components Of Restructuring Liability

As of September 30, 2012, the components of these liabilities are summarized in the following table (in thousands):



	Employee Severance And Other Benefits			Facility Charges			Asset Impairment, net of sales			Legal and Other Fees			Total
Ending accrual balance as of December 31, 2011	$	6		$	13,921		$	—		$	51		$	13,978
Restructuring charge (credit)	1,046			866			(180		)	(28		)	1,704
Cash payments	(909		)	(4,451		)	—			(3		)	(5,363		)
Adjustments or non-cash credits	(10		)	—			(697		)	—			(707		)
Proceeds from sale of assets	—			—			877			—			877
Ending accrual balance as of September 30, 2012	$	133		$	10,336		$	—		$	20		$	10,489

Concurrent Debt and Equity Offerings (Tables)

9 Months Ended

Sep. 30, 2012

Debt and Equity Offerings [Abstract]

Schedule of Long-term Debt Instruments [Table Text Block]

The following is a summary of the liability component of the 2019 Notes as of September 30, 2012 (in thousands):



	September 30, 2012
Net carrying amount of the liability component	$	151,024
Unamortized discount of the liability component	$	136,476
Face Value of the 2019 Notes	$	287,500

- Definition

Tabular disclosure of long-debt instruments or arrangements, including identification, terms, features, collateral requirements and other information necessary to a fair presentation. These are debt arrangements that originally required repayment more than twelve months after issuance or greater than the normal operating cycle of the entity, if longer.

+ References

Reference 1: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 210
-SubTopic 10
-Section S99
-Paragraph 1
-Subparagraph (SX 210.5-02.22)
-URI http://asc.fasb.org/extlink&oid=6877327&loc=d3e13212-122682

Reference 2: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 942
-SubTopic 470
-Section 50
-Paragraph 3
-URI http://asc.fasb.org/extlink&oid=6479336&loc=d3e64711-112823

Reference 3: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 505
-SubTopic 10
-Section 50
-Paragraph 3
-URI http://asc.fasb.org/extlink&oid=6928386&loc=d3e21475-112644

Reference 4: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 235
-SubTopic 10
-Section S99
-Paragraph 1
-Subparagraph (SX 210.4-08.(e),(f))
-URI http://asc.fasb.org/extlink&oid=6881521&loc=d3e23780-122690

Reference 5: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 835
-SubTopic 30
-Section 55
-Paragraph 8
-URI http://asc.fasb.org/extlink&oid=6584090&loc=d3e28878-108400

Reference 6: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 505
-SubTopic 10
-Section 50
-Paragraph 8
-URI http://asc.fasb.org/extlink&oid=6928386&loc=d3e21538-112644

Reference 7: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 835
-SubTopic 30
-Section 45
-Paragraph 1A
-URI http://asc.fasb.org/extlink&oid=6451184&loc=d3e28541-108399

Reference 8: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 505
-SubTopic 10
-Section 50
-Paragraph 6
-URI http://asc.fasb.org/extlink&oid=6928386&loc=d3e21506-112644

Reference 9: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 835
-SubTopic 30
-Section 45
-Paragraph 2
-URI http://asc.fasb.org/extlink&oid=6451184&loc=d3e28551-108399

Reference 10: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 505
-SubTopic 10
-Section 50
-Paragraph 7
-URI http://asc.fasb.org/extlink&oid=6928386&loc=d3e21521-112644

Reference 11: http://www.xbrl.org/2003/role/presentationRef
-Publisher SEC
-Name Regulation S-X (SX)
-Number 210
-Section 02
-Paragraph 22
-Article 5

+ Details

Organization and Summary of Significant Accounting Policies (Narrative) (Details) - USD ($) $ in Millions	9 Months Ended
	Sep. 30, 2012	Sep. 30, 2011
Operations [Line Items]
Unrealized loss position of all securities in years	1 year
Amount written-down for property and equipment	$ 0.3	$ 0.3
Minimum [Member]
Operations [Line Items]
Fiscal year, duration	P52W
Maximum [Member]
Operations [Line Items]
Fiscal year, duration	P53W

Organization and Summary of Significant Accounting Policies (Schedule of Available-for-Sale Securities) (Details) - USD ($) $ in Thousands	Sep. 30, 2012	Dec. 31, 2011
Schedule of Available-for-sale Securities [Line Items]
Available-for-sale securities, Amortized Cost	$ 674,727	$ 283,858
Available-for-sale securities, Gross Unrealized Gains	84	36
Available-for-sale securities, Gross Unrealized Losses	(103)	(173)
Available-for-sale securities, Fair Value	674,708	283,721
Long-Term Investments [Member]
Schedule of Available-for-sale Securities [Line Items]
Available-for-sale securities, Amortized Cost	162,195	85,260
Available-for-sale securities, Gross Unrealized Gains	12	0
Available-for-sale securities, Gross Unrealized Losses	(33)	0
Available-for-sale securities, Fair Value	162,174	85,260
Money Market Funds [Member]
Schedule of Available-for-sale Securities [Line Items]
Available-for-sale securities, Amortized Cost	139,645	81,986
Available-for-sale securities, Gross Unrealized Gains	7	0
Available-for-sale securities, Gross Unrealized Losses	(4)	0
Available-for-sale securities, Fair Value	139,648	81,986
Commercial Paper [Member]
Schedule of Available-for-sale Securities [Line Items]
Available-for-sale securities, Amortized Cost	258,942	29,079
Available-for-sale securities, Gross Unrealized Gains	17	2
Available-for-sale securities, Gross Unrealized Losses	0	(1)
Available-for-sale securities, Fair Value	258,959	29,080
Corporate Bonds [Member]
Schedule of Available-for-sale Securities [Line Items]
Available-for-sale securities, Amortized Cost	162,787	116,068
Available-for-sale securities, Gross Unrealized Gains	44	22
Available-for-sale securities, Gross Unrealized Losses	(94)	(169)
Available-for-sale securities, Fair Value	162,737	115,921
U.S. Government Sponsored Enterprises [Member]
Schedule of Available-for-sale Securities [Line Items]
Available-for-sale securities, Amortized Cost	81,787	37,237
Available-for-sale securities, Gross Unrealized Gains	16	12
Available-for-sale securities, Gross Unrealized Losses	(2)	0
Available-for-sale securities, Fair Value	81,801	37,249
Municipal Bonds [Member]
Schedule of Available-for-sale Securities [Line Items]
Available-for-sale securities, Amortized Cost	31,566	19,488
Available-for-sale securities, Gross Unrealized Gains	0	0
Available-for-sale securities, Gross Unrealized Losses	(3)	(3)
Available-for-sale securities, Fair Value	31,563	19,485
Cash Equivalents [Member]
Schedule of Available-for-sale Securities [Line Items]
Available-for-sale securities, Amortized Cost	308,804	74,256
Available-for-sale securities, Gross Unrealized Gains	1	1
Available-for-sale securities, Gross Unrealized Losses	0	0
Available-for-sale securities, Fair Value	308,805	74,257
Marketable Securities [Member]
Schedule of Available-for-sale Securities [Line Items]
Available-for-sale securities, Amortized Cost	163,543	120,143
Available-for-sale securities, Gross Unrealized Gains	64	35
Available-for-sale securities, Gross Unrealized Losses	(66)	(173)
Available-for-sale securities, Fair Value	163,541	120,005
Restricted Cash And Investments [Member]
Schedule of Available-for-sale Securities [Line Items]
Available-for-sale securities, Amortized Cost	40,185	4,199
Available-for-sale securities, Gross Unrealized Gains	7	0
Available-for-sale securities, Gross Unrealized Losses	(4)	0
Available-for-sale securities, Fair Value	$ 40,188	$ 4,199

(Summary of Available-for-Sale Securities by Contractual Maturity) (Details) - USD ($) $ in Thousands	Sep. 30, 2012	Dec. 31, 2011
Organization, Consolidation and Presentation of Financial Statements [Abstract]
Available-for-sale Securities, Mature in less than one year, Amortized Cost Basis	$ 555,899	$ 259,209
Available-for-sale Securities, Mature in less than one year, Gross Unrealized Gains	65	24
Available-for-sale Securities, Mature in less than one year, Gross Unrealized Losses	(67)	(151)
Available-for-sale Securities, Mature in less than one year, Fair Value	555,897	259,082
Available-for-sale Securities, Mature in one to two years, Amortized Cost Basis	118,828	24,649
Available-for-sale Securities, Mature in one to two years, Gross Unrealized Gains	19	12
Available-for-sale Securities, Mature in one to two years, Gross Unrealized Losses	(36)	(22)
Available-for-sale Securities, Mature in one to two years, Fair Value	118,811	24,639
Available-for-sale Securities, Amortized Cost Basis	674,727	283,858
Available-for-sale Securities, Gross Unrealized Gains	84	36
Available-for-sale Securities, Gross Unrealized Losses	(103)	(173)
Available-for-sale securities, Fair Value	$ 674,708	$ 283,721

Organization and Summary of Significant Accounting Policies (Schedule of Fair Value of Financial Assets Measured on a Recurring Basis) (Details) - USD ($) $ in Thousands	Sep. 30, 2012	Dec. 31, 2011
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Total fair value of financial assets	$ 674,708	$ 283,721
Money Market Funds [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Total fair value of financial assets	139,648	81,986
Commercial Paper [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Total fair value of financial assets	258,959	29,080
Corporate Bonds [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Total fair value of financial assets	162,737	115,921
U.S. Government Sponsored Enterprises [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Total fair value of financial assets	81,801	37,249
Municipal Bonds [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Total fair value of financial assets	31,563	19,485
Level 1 [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Total fair value of financial assets	139,648	81,986
Level 1 [Member] \| Money Market Funds [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Total fair value of financial assets	139,648	81,986
Level 1 [Member] \| Commercial Paper [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Total fair value of financial assets	0	0
Level 1 [Member] \| Corporate Bonds [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Total fair value of financial assets	0	0
Level 1 [Member] \| U.S. Government Sponsored Enterprises [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Total fair value of financial assets	0	0
Level 1 [Member] \| Municipal Bonds [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Total fair value of financial assets	0	0
Level 2 [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Total fair value of financial assets	535,060	201,735
Level 2 [Member] \| Money Market Funds [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Total fair value of financial assets	0	0
Level 2 [Member] \| Commercial Paper [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Total fair value of financial assets	258,959	29,080
Level 2 [Member] \| Corporate Bonds [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Total fair value of financial assets	162,737	115,921
Level 2 [Member] \| U.S. Government Sponsored Enterprises [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Total fair value of financial assets	81,801	37,249
Level 2 [Member] \| Municipal Bonds [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Total fair value of financial assets	31,563	19,485
Fair Value, Inputs, Level 3 [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Total fair value of financial assets	0	0
Fair Value, Inputs, Level 3 [Member] \| Money Market Funds [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Total fair value of financial assets	0	0
Fair Value, Inputs, Level 3 [Member] \| Commercial Paper [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Total fair value of financial assets	0	0
Fair Value, Inputs, Level 3 [Member] \| Corporate Bonds [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Total fair value of financial assets	0	0
Fair Value, Inputs, Level 3 [Member] \| U.S. Government Sponsored Enterprises [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Total fair value of financial assets	0	0
Fair Value, Inputs, Level 3 [Member] \| Municipal Bonds [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Total fair value of financial assets	$ 0	$ 0

Organization and Summary of Significant Accounting Policies (Schedule of Estimated Fair Value of Outstanding Debt) (Details) - USD ($)	Sep. 30, 2012	Aug. 14, 2012	Dec. 31, 2011
Debt Instrument [Line Items]
Fair value of outstanding debt	$ 389,887,000		$ 87,901,000
Equipment Lines Of Credit [Member]
Debt Instrument [Line Items]
Fair value of outstanding debt	6,006,000		10,066,000
Silicon Valley Bank Loan [Member]
Debt Instrument [Line Items]
Fair value of outstanding debt	77,981,000		77,835,000
Senior Notes [Member] \| 4.25% Convertible Senior Subordinated Notes due August 15, 2019 [Member]
Debt Instrument [Line Items]
Debt instrument, face value	287,500,000	$ 287,500,000
Debt instrument, interest rate		4.25%
Fair value of outstanding debt	$ 305,900,000	$ 149,200,000	$ 0

(Schedule of Potential Shares of Common Stock Excluded from Computation of Diluted Net Loss Per Share) (Details) - USD ($) $ / shares in Units, $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2012	Sep. 30, 2011	Sep. 30, 2012	Sep. 30, 2011
Numerator:
Net (loss) income	$ (32,814)	$ 77,865	$ (95,452)	$ 29,401
Denominator
Shares used in computing basic (loss) income per share amounts	166,354,000	129,145,000	152,316,000	123,426,000
Add effect of dilutive securities:
Shares issuable upon conversion of our GlaxoSmithKline loan	0	449,000	0	1,568,000
Shares issuable upon the exercise of outstanding stock options	0	1,444,000	0	3,471,000
Shares issuable pursuant to the issuance of vested RSUs	0	144,000	0	558,000
Shares issuable pursuant to the exercise of warrants	0	48,000	0	281,000
Shares issuable upon the purchase of ESPP	0	114,000	0	126,000
Shares used in computing diluted net (loss) income per common share	0	2,199,000	0	6,004,000
Shares used in computing diluted (loss) income per share amounts	166,354,000	131,344,000	152,316,000	129,430,000
Net (loss) income per share, basic, in dollars per share	$ (0.20)	$ 0.60	$ (0.63)	$ 0.24
Net (loss) income per share, diluted, in dollars per share	$ (0.20)	$ 0.59	$ (0.63)	$ 0.23
Antidilutive shares excluded from Earnings Per Share calculation		15,500,000	71,900,000	7,400,000
Convertible Debt Securities [Member]
Add effect of dilutive securities:
Antidilutive shares excluded from Earnings Per Share calculation			54,100,000
Stock Compensation Plan [Member]
Add effect of dilutive securities:
Antidilutive shares excluded from Earnings Per Share calculation			17,700,000

Stock-Based Compensation (Narrative) (Details) $ in Millions	9 Months Ended
	Sep. 30, 2012 USD ($)
Stock Options [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Unrecognized compensation expense	$ 16.0
Unrecognized compensation expense, weighted-average period for recognition (in years)	3 years 1 month 2 days
Restricted Stock Units (RSUs) [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Unrecognized compensation expense	$ 6.8
Unrecognized compensation expense, weighted-average period for recognition (in years)	3 years 22 days

Stock-Based Compensation (Schedule of Allocated Employee Stock-Based Compensation Expenses) (Details) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2012	Sep. 30, 2011	Sep. 30, 2012	Sep. 30, 2011
Employee Service Share-based Compensation, Allocation of Recognized Period Costs [Line Items]
Total employee stock-based compensation expense	$ 1,893	$ 2,955	$ 6,172	$ 9,284
Research And Development Expense [Member]
Employee Service Share-based Compensation, Allocation of Recognized Period Costs [Line Items]
Total employee stock-based compensation expense	970	1,378	3,202	4,557
General And Administrative Expense [Member]
Employee Service Share-based Compensation, Allocation of Recognized Period Costs [Line Items]
Total employee stock-based compensation expense	923	1,401	2,970	4,102
Restructuring-Related Stock Compensation Expense [Member]
Employee Service Share-based Compensation, Allocation of Recognized Period Costs [Line Items]
Total employee stock-based compensation expense	$ 0	$ 176	$ 0	$ 625

- Definition

Represents the expense recognized during the period arising from equity-based compensation arrangements (for example, shares of stock, unit, stock options or other equity instruments) with employees, directors and certain consultants qualifying for treatment as employees.

+ References + Details

Stock-Based Compensation (Schedule of Fair Value of Employee Share-Based Payments Awards Estimated Using the Assumptions and Weighted Average Fair Values) (Details) - $ / shares	3 Months Ended		9 Months Ended
	Sep. 30, 2012	Sep. 30, 2011	Sep. 30, 2012	Sep. 30, 2011
Stock Options [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Weighted average grant date fair value	$ 3.31	$ 3.28	$ 3.27	$ 3.52
Risk-free interest rate	0.81%	0.97%	0.82%	1.05%
Dividend yield	0.00%	0.00%	0.00%	0.00%
Volatility	69.00%	70.00%	69.00%	70.00%
Expected life	5 years 7 months 6 days	5 years 4 months 24 days	5 years 8 months	5 years 6 months
Employee Stock Purchase Plan [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Weighted average grant date fair value	$ 1.63	$ 4.24	$ 2.13	$ 3.05
Risk-free interest rate	0.15%	0.10%	0.10%	0.13%
Dividend yield	0.00%	0.00%	0.00%	0.00%
Volatility	68.00%	70.00%	68.00%	68.00%
Expected life	6 months	6 months	6 months	6 months

Stock-Based Compensation (Summary of All Stock Option Activity) (Details)	9 Months Ended
	Sep. 30, 2012 USD ($) $ / shares shares
Share-based Compensation [Abstract]
Options outstanding at beginning of period, Shares \| shares	17,436,378
Granted, Shares \| shares	3,300,546
Exercised, Shares \| shares	(175,708)
Cancelled, Shares \| shares	(1,399,526)
Options outstanding at end of period, Shares \| shares	19,161,690
Exercisable at end of period, Shares \| shares	13,559,920
Options outstanding at beginning of period, Weighted Average Exercise Price \| $ / shares	$ 7.16
Granted, Weighted Average Exercise Price \| $ / shares	5.49
Exercised, Weighted Average Exercise Price \| $ / shares	5.12
Cancelled, Weighted Average Exercise Price \| $ / shares	7.92
Options outstanding at end of period, Weighted Average Exercise Price \| $ / shares	6.84
Exercisable at end of period, Weighted Average Exercise Price \| $ / shares	$ 7.32
Options outstanding at end of period, Weighted Average Remaining Contractual Term	4 years 7 months 21 days
Exercisable at end of period, Weighted Average Remaining Contractual Term	3 years 9 months 18 days
Options outstanding at end of period, Aggregate Intrinsic Value, in dollars \| $	$ 287,800
Exercisable at end of period, Aggregate Intrinsic Value, in dollars \| $	$ 239,408

(Summary of All RSU Activity) (Details) - Restricted Stock Units (RSUs) [Member]	9 Months Ended
	Sep. 30, 2012 USD ($) $ / shares shares
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
RSUs outstanding at beginning of period, Shares \| shares	1,391,691
Awarded, Shares \| shares	711,575
Released, Shares \| shares	(459,416)
Forfeited, Shares \| shares	(201,987)
RSUs outstanding at end of period, Shares \| shares	1,441,863
RSUs outstanding at beginning of period, Weighted Average Grant Date Fair Value \| $ / shares	$ 6.92
Awarded, Weighted Average Grant Date Fair Value \| $ / shares	5.53
Released, Weighted Average Grant Date Fair Value \| $ / shares	7.33
Forfeited, Weighted Average Grant Date Fair Value \| $ / shares	6.74
RSUs outstanding at end of period, Weighted Average Grant Date Fair Value \| $ / shares	$ 6.13
ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsOutstandingWeightedAverageRemainingContractualTerms	1 year 10 months 2 days
RSUs outstanding at end of period, Aggregate Intrinsic Value, in dollars \| $	$ 6,956,995

Collaborations (Details) $ in Thousands	1 Months Ended							3 Months Ended			9 Months Ended		23 Months Ended
Collaborations (Details) $ in Thousands	Jan. 19, 2012 USD ($)	Dec. 31, 2011 USD ($)	Jul. 31, 2011 USD ($)	Nov. 30, 2010 USD ($)	Dec. 31, 2008 USD ($)	Feb. 29, 2008 USD ($)	Jan. 31, 2007 USD ($) compound	Sep. 30, 2012 USD ($)	Mar. 31, 2012 USD ($)	Sep. 30, 2011 USD ($)	Sep. 30, 2012 USD ($)	Sep. 30, 2011 USD ($)	Sep. 30, 2012 USD ($)
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
License								$ 4,012		$ 122,703	$ 22,702	$ 167,984
Merck [Member]
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
License		$ 1,300							$ 10,700
Upfront cash payment	$ 12,000
Potential development and regulatory milestone payments											239,000
Maximum amount eligible for sales performance milestones											375,000
2007 Cancer Collaboration [Member] \| Bristol-Myers Squibb [Member]
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Upfront cash payment							$ 60,000
Number of future drug compounds to be selected \| compound							3
Number of future drug compounds available for selection \| compound							6
Selected milestone earnings entitled and received					$ 20,000	$ 20,000
Collaboration agreement opt-out consideration payment				$ 20,000
TGR5 License Agreement [Member] \| Bristol-Myers Squibb [Member]
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Upfront cash payment				35,000
Maximum amount eligible for development and regulatory milestones				250,000
Maximum amount eligible for commercial milestones under collaborations agreement				150,000
Aggregate license revenue													$ 24,100
ROR Collaboration Agreement [Member] \| Bristol-Myers Squibb [Member]
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Upfront cash payment				5,000
Maximum amount eligible for development and regulatory milestones				255,000
Maximum amount eligible for commercial milestones under collaborations agreement				$ 150,000
Revenue Recognition, Milestone Method, Revenue Recognized			$ 2,500
Aggregate license revenue											$ 5,300
Collaborative Arrangement, Product [Member] \| 2007 Cancer Collaboration [Member] \| Bristol-Myers Squibb [Member]
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Periodic revenue under milestone method							$ 20,000

Restructurings (Narrative) (Details) $ in Thousands	3 Months Ended		9 Months Ended		12 Months Ended	33 Months Ended
Restructurings (Narrative) (Details) $ in Thousands	Sep. 30, 2012 USD ($) employee	Sep. 30, 2011 USD ($)	Sep. 30, 2012 USD ($) employee facility	Sep. 30, 2011 USD ($)	Dec. 31, 2010 employee plan	Sep. 30, 2012 USD ($) employee
Restructuring Cost and Reserve [Line Items]
Number of restructuring plans \| plan					2
Overall reduction of employees \| employee					386
Aggregate reduction in headcount \| employee	422		422			422
Aggregate restructuring charges	$ 733	$ 2,937	$ 1,704	$ 6,190		$ 44,600
Number of facilities exited \| facility			3
Expected additional payment for restructuring			$ 1,300
Termination Benefits [Member]
Restructuring Cost and Reserve [Line Items]
Aggregate restructuring charges						21,300
Facility-Charges And Impairment Of Various Assets [Member]
Restructuring Cost and Reserve [Line Items]
Aggregate restructuring charges						$ 23,300

Restructurings (Summary of Components of Restructuring Liability) (Details) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended		33 Months Ended
	Sep. 30, 2012	Sep. 30, 2011	Sep. 30, 2012	Sep. 30, 2011	Sep. 30, 2012
Restructuring Reserve [Roll Forward]
Ending accrual balance as of December 31, 2011			$ 13,978
Restructuring charge	$ 733	$ 2,937	1,704	$ 6,190	$ 44,600
Cash payments			(5,363)
Adjustments or non-cash credits			(707)
Proceeds from sale of assets			877	$ 0
Ending accrual balance as of September 30, 2012	10,489		10,489		10,489
Employee Severance And Other Benefits [Member]
Restructuring Reserve [Roll Forward]
Ending accrual balance as of December 31, 2011			6
Restructuring charge			1,046
Cash payments			(909)
Adjustments or non-cash credits			(10)
Proceeds from sale of assets			0
Ending accrual balance as of September 30, 2012	133		133		133
Facility Charges [Member]
Restructuring Reserve [Roll Forward]
Ending accrual balance as of December 31, 2011			13,921
Restructuring charge			866
Cash payments			(4,451)
Adjustments or non-cash credits			0
Proceeds from sale of assets			0
Ending accrual balance as of September 30, 2012	10,336		10,336		10,336
Asset Impairment [Member]
Restructuring Reserve [Roll Forward]
Ending accrual balance as of December 31, 2011			0
Restructuring charge			(180)
Cash payments			0
Adjustments or non-cash credits			(697)
Proceeds from sale of assets			877
Ending accrual balance as of September 30, 2012	0		0		0
Legal And Other Fees [Member]
Restructuring Reserve [Roll Forward]
Ending accrual balance as of December 31, 2011			51
Restructuring charge			(28)
Cash payments			(3)
Adjustments or non-cash credits			0
Proceeds from sale of assets			0
Ending accrual balance as of September 30, 2012	$ 20		$ 20		$ 20

Sale of Shares of Common Stock (Details) - USD ($) $ in Thousands		1 Months Ended		9 Months Ended
	Aug. 14, 2012	Feb. 29, 2012	Mar. 31, 2011	Sep. 30, 2012	Sep. 30, 2011
Equity [Abstract]
Public offering of common stock	34,500,000	12,700,000	17,300,000
Net proceeds from public offering		$ 65,000	$ 179,300	$ 203,479	$ 179,377

Concurrent Debt and Equity Offerings (Details)

1 Months Ended

3 Months Ended

9 Months Ended

Aug. 14, 2012

USD ($)

$ / shares

Feb. 29, 2012

Mar. 31, 2011

Sep. 30, 2012

USD ($)

payment

Sep. 30, 2012

USD ($)

payment

Sep. 30, 2011

USD ($)

Dec. 31, 2011

USD ($)

Debt and Equity Offerings [Line Items]

Public offering of common stock | shares

34,500,000

12,700,000

17,300,000

Share price | $ / shares

$ 4.25

Proceeds from concurrent offerings

$ 416,100,000

Proceeds from convertible debt offering

277,700,000

$ 277,673,000

$ 0

Payments for underwriting discount, debt

9,300,000

Payments of debt issuance costs

500,000

Net proceeds from public offering

138,400,000

Payments for underwriting ciscount, equity

7,700,000

Equity offering discount

500,000

Short-term restricted cash and investments

$ 12,242,000

12,242,000

$ 0

^[1]

Long-term restricted cash and investments

27,946,000

4,199,000

^[1]

Fair value of outstanding debt

389,887,000

87,901,000

Adjustments to additional paid in capital, equity issuance costs

4,700,000

Debt Payment [Member]

Debt and Equity Offerings [Line Items]

Restricted cash and investments

36,500,000

Short-term restricted cash and investments

12,200,000

Long-term restricted cash and investments

24,300,000

4.25% Convertible Senior Subordinated Notes due August 15, 2019 [Member] | Senior Notes [Member]

Debt and Equity Offerings [Line Items]

Debt instrument, face value

$ 287,500,000

Debt instrument, interest rate

4.25%

Debt, redemption price component, percentage of principal

100.00%

Convertible debt, conversion ratio | shares

188.2353

Convertible debt, principal for conversion ratio

$ 1,000

Convertible debt, equivalent conversion price | $ / shares

$ 5.31

Debt, number of payments secured in escrow | payment

Convertible debt, effective interest rate on liability component

10.00%

Fair value of outstanding debt

$ 149,200,000

$ 305,900,000

$ 0

Debt instrument, unamortized discount

$ 138,300,000

136,476,000

Convertible debt, carrying amount of liability component

151,024,000

Interest expense based on stated interest rate

3,200,000

Non-cash amortization of debt discount and offering costs

1,800,000

4.25% Convertible Senior Subordinated Notes due August 15, 2019 [Member] | Senior Notes [Member] | Other Long-term Assets [Member]

Debt and Equity Offerings [Line Items]

Unamortized debt issuance expense

$ 5,100,000

[1]	The condensed consolidated balance sheet at December 31, 2011 has been derived from the audited consolidated financial statements at that date but does not include all of the information and footnotes required by U.S. generally accepted accounting principles for complete financial statements.

Deerfield Financing (Details) - Secured Convertible Notes Due June 2015 [Member] - Deerfield Financing [Member] - USD ($) $ in Millions	Jun. 30, 2010	Sep. 30, 2012	Aug. 06, 2012
Debt Instrument [Line Items]
Debt instrument, face value	$ 124.0
Debt instruments, purchase price	80.0
Debt instruments, closing fees and expenses	2.0
Annual interest	$ 6.0
Percentage of revenues payable under collaborative arrangements in 2013, 2014 and 2015	15.00%
Maximum prepayment amount under collaborative arrangements in 2013 and 2014	$ 27.5
Minimum prepayment amount under collaborative arrangements	10.0
Minimum limit on prepayments	5.0
Debt instrument, minimum purchase amount for prepayment condition	$ 400.0
Percentage of assets minimum for prepayment condition	50.00%
Balance of unamortized closing fees and expenses		$ 1.1
Carrying value of the loan		$ 98.2
Other Long-term Assets [Member]
Debt Instrument [Line Items]
Debt instrument, consent fee			$ 1.5

Income Taxes (Details) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
Income Taxes (Details) - USD ($) $ in Thousands	Sep. 30, 2012	Sep. 30, 2011	Sep. 30, 2012	Sep. 30, 2011
Income Taxes [Line Items]
Provision for income tax	$ 10	$ 0	$ 33	$ 0
Deferred Income Tax Expense (Benefit)	54,400
Other Liabilities, Noncurrent [Member]
Income Taxes [Line Items]
Deferred Tax Liabilities, Net, Noncurrent	400		400
Prepaid Expenses and Other Current Assets [Member]
Income Taxes [Line Items]
Deferred Tax Assets, Net of Valuation Allowance, Noncurrent	$ 400		$ 400

- Definition

The component of income tax expense for the period representing the increase (decrease) in the entity's deferred tax assets and liabilities pertaining to continuing operations.

+ References

Reference 1: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 230
-SubTopic 10
-Section 45
-Paragraph 28
-Subparagraph (b)
-URI http://asc.fasb.org/extlink&oid=6943989&loc=d3e3602-108585

Reference 2: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Glossary Deferred Tax Expense (or Benefit)
-URI http://asc.fasb.org/extlink&oid=6510177

Reference 3: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 740
-SubTopic 10
-Section 50
-Paragraph 9
-Subparagraph (b)
-URI http://asc.fasb.org/extlink&oid=6907707&loc=d3e32639-109319

Reference 4: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 235
-SubTopic 10
-Section S99
-Paragraph 1
-Subparagraph (SX 210.4-08.(h))
-URI http://asc.fasb.org/extlink&oid=6881521&loc=d3e23780-122690

Reference 5: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 740
-SubTopic 10
-Section S99
-Paragraph 1
-Subparagraph (SAB TOPIC 6.I.7)
-URI http://asc.fasb.org/extlink&oid=6889476&loc=d3e330036-122817

Reference 6: http://www.xbrl.org/2003/role/presentationRef
-Publisher SEC
-Name Regulation S-X (SX)
-Number 210
-Section 08
-Paragraph h
-Article 4

Reference 7: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Statement of Financial Accounting Standard (FAS)
-Number 109
-Paragraph 289
-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

Reference 8: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Statement of Financial Accounting Standard (FAS)
-Number 109
-Paragraph 45
-Subparagraph b
-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

Reference 9: http://www.xbrl.org/2003/role/presentationRef
-Publisher SEC
-Name Staff Accounting Bulletin (SAB)
-Number Topic 6
-Section I
-Subsection 7

Reference 10: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Statement of Financial Accounting Standard (FAS)
-Number 95
-Paragraph 28
-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

+ Details

- Definition

Amount after allocation of valuation allowances of deferred tax asset attributable to deductible temporary differences and carryforwards expected to be realized or consumed within one year or operating cycle, if longer.

+ References + Details