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Document And Entity Information - shares	9 Months Ended
Document And Entity Information - shares	Sep. 30, 2014	Oct. 29, 2014
Document And Entity Information [Abstract]
Document Type	10-Q
Amendment Flag	false
Document Period End Date	Sep. 30, 2014
Document Fiscal Year Focus	2014
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	--01-02
Entity Common Stock, Shares Outstanding		195,215,795

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

Sep. 30, 2014

Dec. 31, 2013

^[1]

Current assets:

Cash and cash equivalents

$ 100,065

$ 103,978

Short-term investments

91,937

138,475

Short-term restricted cash and investments

12,210

12,213

Trade and other receivables

4,722

3,941

Inventory

3,876

2,890

Prepaid expenses and other current assets

7,860

5,112

Total current assets

220,670

266,609

Long-term investments

84,589

144,299

Long-term restricted cash and investments

4,684

16,897

Property and equipment, net

2,928

4,910

Goodwill

63,684

Other assets

7,101

6,888

Total assets

383,656

503,287

Current liabilities:

Accounts payable

3,362

9,345

Accrued clinical trial liabilities

45,102

34,958

Accrued compensation and benefits

6,441

12,797

Other accrued liabilities

13,855

13,116

Current portion of convertible notes

96,496

10,000

Current portion of loans payable

757

1,762

Current portion of restructuring

6,580

4,425

Deferred revenue

1,319

1,450

Total current liabilities

173,912

87,853

Long-term portion of convertible notes

177,962

255,147

Long-term portion of loans payable

80,000

80,328

Long-term portion of restructuring

5,521

9,047

Other long-term liabilities

4,772

4,674

Total liabilities

442,167

437,049

Commitments

Stockholders’ (deficit) equity:

Preferred stock

Common stock, $0.001 par value; 400,000,000 shares authorized; issued and outstanding: 195,179,456 and 184,533,651 shares at September 30, 2014 and December 31, 2013, respectively

195

184

Additional paid-in capital

1,650,621

1,564,670

Accumulated other comprehensive income

146

Accumulated deficit

(1,709,351)

(1,498,762)

Total stockholders’ (deficit) equity

(58,511)

66,238

Total liabilities and stockholders’ (deficit) equity

$ 383,656

$ 503,287

[1]	The condensed consolidated balance sheet as of December 31, 2013 has been derived from the audited financial statements as of that date.

Condensed Consolidated Balance Sheets (Parenthetical) - $ / shares	Sep. 30, 2014	Dec. 31, 2013
Statement of Financial Position [Abstract]
Common stock, par value, in dollars per share	$ 0.001	$ 0.001
Common stock, shares authorized	400,000,000	400,000,000
Common stock, shares issued	195,179,456	184,533,651
Common stock, shares outstanding	195,179,456	184,533,651

Condensed Consolidated Statements Of Operations - USD ($) shares in Thousands, $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2014	Sep. 30, 2013	Sep. 30, 2014	Sep. 30, 2013
Revenues:
Net product revenues	$ 6,291	$ 4,771	$ 17,758	$ 10,670
License and contract revenues	0	695	0	16,321
Total revenues	6,291	5,466	17,758	26,991
Operating expenses:
Cost of goods sold	573	290	1,359	855
Research and development	43,628	47,354	149,451	129,166
Selling, general and administrative	9,906	13,598	41,063	37,323
Restructuring charge	3,758	137	4,135	865
Total operating expenses	57,865	61,379	196,008	168,209
Loss from operations	(51,574)	(55,913)	(178,250)	(141,218)
Other income (expense), net:
Interest income and other, net	1,296	219	3,786	930
Interest expense	(12,282)	(11,430)	(36,125)	(33,726)
Total other income (expense), net	(10,986)	(11,211)	(32,339)	(32,796)
Net loss	$ (62,560)	$ (67,124)	$ (210,589)	$ (174,014)
Net loss per share, basic and diluted, in dollars per share	$ (0.32)	$ (0.36)	$ (1.09)	$ (0.95)
Shares used in computing basic and diluted net loss per share, in shares	195,126	184,149	193,855	183,957

Condensed Consolidated Statements of Comprehensive Loss - USD ($)
$ in Thousands

3 Months Ended

9 Months Ended

Sep. 30, 2014

Sep. 30, 2013

Sep. 30, 2014

Sep. 30, 2013

Statement of Comprehensive Income [Abstract]

Net loss

$ (62,560)

$ (67,124)

$ (210,589)

$ (174,014)

Other comprehensive income (loss)

^[1]

(153)

443

(122)

272

Comprehensive loss

$ (62,713)

$ (66,681)

$ (210,711)

$ (173,742)

[1]

Other comprehensive income (loss) consisted solely of unrealized gains or losses, net on available for sale securities arising during the periods presented. There were no reclassification adjustments to net loss resulting from realized gains or losses on the sale of securities and there was no income tax expense related to other comprehensive income during those periods.

- Definition

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

+ References + Details

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

9 Months Ended

Sep. 30, 2014

Sep. 30, 2013

Cash flows from operating activities:

Net loss

$ (210,589)

$ (174,014)

Adjustments to reconcile net loss to net cash used in operating activities:

Depreciation and amortization

3,014

2,382

Stock-based compensation expense

8,454

8,503

Restructuring Costs and Asset Impairment Charges

667

Accretion of debt discount

21,826

19,445

Gain on sale of business

(838)

Changes in the fair value of warrants

(1,916)

Other

3,602

5,243

Changes in assets and liabilities:

Trade and other receivables

(781)

(2,420)

Inventory

(986)

(1,764)

Prepaid expenses and other assets

(2,834)

(1,495)

Accounts payable, accrued compensation, and other accrued liabilities

(11,600)

(652)

Clinical trial liabilities

10,144

14,482

Restructuring liability

(2,705)

(5,320)

Other long-term liabilities

(756)

(530)

Deferred revenue

(131)

(15,304)

Net cash used in operating activities

(185,429)

(151,444)

Cash flows from investing activities:

Purchases of property and equipment

(452)

(2,079)

Proceeds from sale of property and equipment

286

Proceeds from sale of business

838

Proceeds from maturities of restricted cash and investments

20,397

15,968

Purchase of restricted cash and investments

(8,184)

(3,785)

Proceeds from maturities of investments

212,506

251,470

Purchases of investments

(109,237)

(176,768)

Net cash provided by investing activities

116,154

84,846

Cash flows from financing activities:

Proceeds from issuance of common stock, net

75,646

Proceeds from exercise of stock options and warrants

120

Proceeds from employee stock purchase plan

929

894

Principal payments on debt

(11,333)

(12,374)

Net cash provided by (used in) financing activities

65,362

(11,455)

Net decrease in cash and cash equivalents

(3,913)

(78,053)

Cash and cash equivalents at beginning of period

103,978

^[1]

170,069

Cash and cash equivalents at end of period

100,065

92,016

Supplemental cash flow disclosure - non-cash financing activity:

Issuance of warrants in connection with amendment to convertible notes

$ 2,762

$ 0

[1]	The condensed consolidated balance sheet as of December 31, 2013 has been derived from the audited financial statements as of that date.

Organization and Summary of Significant Accounting Policies	9 Months Ended
	Sep. 30, 2014
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 biopharmaceutical company committed to developing small molecule therapies for the treatment of cancer. Our two most advanced assets are cabozantinib, our wholly-owned inhibitor of multiple receptor tyrosine kinases, and cobimetinib (GDC-0973/XL518), a potent, highly selective inhibitor of MEK, which we out-licensed to Genentech (a member of the Roche Group) (“Genentech”). We are focusing our development and commercialization efforts primarily on cabozantinib. We are evaluating cabozantinib in a broad development program comprising over forty-five clinical trials, including three ongoing phase 3 pivotal trials across multiple indications, with particular focus on our phase 3 pivotal trials in metastatic renal cell carcinoma (“RCC”) and advanced hepatocellular carcinoma (“HCC”). Cabozantinib was approved by the United States Food and Drug Administration (“FDA”) on November 29, 2012 for the treatment of progressive, metastatic medullary thyroid cancer (“MTC”) in the United States under the brand name COMETRIQ^(R). COMETRIQ became commercially available in the United States in late January 2013. In March 2014, the European Commission approved cabozantinib for the treatment of adult patients with progressive, unresectable locally advanced or metastatic MTC, also under the brand name COMETRIQ. The European Commission granted conditional marketing authorization following a positive opinion from the European Committee for Medicinal Products for Human Use, issued in December 2013. Our second oncology asset, cobimetinib, is being evaluated by Genentech in a broad development program, including coBRIM, a phase 3 pivotal trial evaluating cobimetinib in combination with vemurafenib in previously untreated patients with unresectable locally advanced or metastatic melanoma harboring a BRAF^V600 mutation. On September 29, 2014, positive results from this trial were reported at the European Society for Medical Oncology 2014 Congress. The trial met its primary endpoint of demonstrating a statistically significant increase in investigator-determined progression-free survival. Roche has completed the Marketing Authorization Application for the combination of cobimetinib and vemurafenib in the European Union. In the United States, cobimetinib has received Fast Track Designation from the FDA, and Genentech expects to complete its New Drug Application filing for the combination before the end of this year. Basis of Consolidation The consolidated financial statements include the accounts of Exelixis and those of our wholly-owned subsidiaries. These entities’ functional currency is the U.S. dollar. All intercompany balances and transactions have been eliminated. Basis of Presentation The accompanying unaudited 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 for complete financial statements. In our opinion, all adjustments (consisting only 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 generally ends on the Friday closest to December 31st. Fiscal year 2013, a 52-week year, ended on December 27, 2013, and fiscal year 2014, a 53-week year, will end on January 2, 2015. For convenience, references in this report as of and for the fiscal periods ended September 26, 2014 and September 27, 2013, and as of the fiscal year ended December 27, 2013, are indicated as ended September 30, 2014, September 30, 2013, and December 31, 2013, respectively. Operating results for the nine months ended September 30, 2014 are not necessarily indicative of the results that may be expected for the fiscal year ending January 2, 2015 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 year ended December 31, 2013, included in our Annual Report on Form 10-K filed with the SEC on February 20, 2014. Segment Information We operate as a single reportable segment. Use of Estimates The preparation of our consolidated financial statements is in conformity with accounting principles generally accepted in the United States which requires management to make judgments, 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 inventory, revenue recognition, valuation of long-lived assets, certain accrued liabilities including clinical trial accruals and restructuring liability, valuation of warrants, share-based compensation and the valuation of the debt and equity components of our convertible debt at issuance. We base our estimates on historical experience and on various other market-specific and other relevant assumptions that we believe 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. Revenue Recognition We recognize revenue from the sale of COMETRIQ and from license fees and milestones earned on research and collaboration arrangements. See “Note 1 - Organization and Summary of Significant Accounting Policies” to our Consolidated Financial Statements included in our Annual Report on Form 10-K for the year ended December 31, 2013 for a description of our policies for revenue recognition on research and collaboration agreements. We did not enter into any new collaboration agreements during the nine months ended September 30, 2014. See “Note 2 - Research and Collaboration Agreements” to our Consolidated Financial Statements included in our Annual Report on Form 10-K for the year ended December 31, 2013 for a description of our existing collaboration agreements. Net Product Revenues We recognize revenue when it is both realized or realizable and earned, meaning persuasive evidence of an arrangement exists, delivery has occurred, title has transferred, the price is fixed or determinable, there are no remaining customer acceptance requirements, and collectability of the resulting receivable is reasonably assured. For product sales in the United States, this generally occurs upon shipment of the product to the patient by our distributor. For product sales in Europe, this occurs when our European distribution partner has accepted the product. We sell our product, COMETRIQ, in the United States to a specialty pharmacy that benefits from customer incentives and has a right of return. We have a limited sales history and cannot reliably estimate expected returns of the product nor the discounts and rebates due to payors at the time of shipment to the specialty pharmacy. Accordingly, upon shipment to the specialty pharmacy, we record deferred revenue on our Consolidated Balance Sheets. We recognize revenue when the specialty pharmacy provides the product to a patient based on the fulfillment of a prescription. We record revenue using an analysis of prescription data from our specialty pharmacy to ascertain the date of shipment and the payor mix. This approach is frequently referred to as the “sell-through” revenue recognition model. Once the prescription has been provided to the patient, it is not subject to return unless the product is damaged. We record revenue at the time our European distribution partner has accepted the product, a method also known as the “sell-in” revenue recognition model. Product Sales Discounts and Allowances We calculate gross product revenues based on the price that we charge our United States specialty pharmacy and our European distribution partner. We estimate our domestic net product revenues by deducting from our gross product revenues (a) trade allowances, such as discounts for prompt payment, (b) estimated government rebates and chargebacks, and (c) estimated costs of patient assistance programs. We initially record estimates for these deductions at the time we recognize the gross revenue. We update our estimates on a recurring basis as new information becomes available. See “Note 1 - Organization and Summary of Significant Accounting Policies” to our Consolidated Financial Statements included in our Annual Report on Form 10-K for the year ended December 31, 2013 for a further description of our discounts and allowances. Our European distribution partner is entitled to receive a project management fee based upon the achievement of a pre-specified revenue goal which, when deemed probable, is ratably accrued as a reduction to gross revenue. Cost of Goods Sold Cost of goods sold is related to our product revenues and consists primarily of a 3% royalty and indirect labor costs, and to a lesser extent, the cost of manufacturing and other third party logistics costs of our product. A significant portion of the manufacturing costs for product sales were incurred prior to regulatory approval of COMETRIQ for the treatment of progressive, metastatic MTC and, therefore, were expensed as research and development costs when those costs were incurred, rather than capitalized as inventory. In accordance with our product development and commercialization agreement with GlaxoSmithKline, we are required to pay GlaxoSmithKline a 3% royalty on the Net Sales of any product incorporating cabozantinib, including COMETRIQ. Net Sales is defined in the product development and commercialization agreement generally as the gross invoiced sales price less customer credits, rebates, chargebacks, shipping costs, customs duties, and sales tax and other similar tax payments we are required to make. Recently Issued Accounting Pronouncements In May 2014, the Financial Accounting Standards Board (“FASB”) issued Accounting Standards Update (“ASU”) 2014-09, Revenue from Contracts with Customers (“ASU 2014-09”). ASU 2014-09 supersedes the revenue recognition requirements of FASB Accounting Standards Codification (“ASC”) Topic 605, Revenue Recognition and most industry-specific guidance throughout the Accounting Standards Codification, resulting in the creation of FASB ASC Topic 606, Revenue from Contracts with Customers. ASU 2014-09 requires entities to recognize revenue in a way that depicts the transfer of promised goods or services to customers in an amount that reflects the consideration to which the entity expects to be entitled to in exchange for those goods or services. Adoption will be permitted using either a retrospective or modified retrospective approach, and is effective for fiscal years, and interim periods within those years, beginning after December 15, 2016. Early adoption is not permitted. We are currently evaluating the impact of adopting this ASU, inclusive of available transitional methods on our consolidated financial statements and related disclosures. In August 2014, the FASB issued ASU 2014-15, Presentation of Financial Statements-Going Concern (“ASU 2014-15”). ASU 2014-15 provides guidance on management’s responsibility in evaluating whether there are conditions or events that raise substantial doubt about a company’s ability to continue as a going concern within one year from the date the financial statements are issued, and about related footnote disclosures. ASU 2014-15 is effective for the annual period ending after December 15, 2016, and for annual periods and interim periods thereafter. Early application is permitted. We are currently evaluating the impact of adopting ASU 2014-15 and its related disclosures.

Restructurings

9 Months Ended

Sep. 30, 2014

Restructuring Charges [Abstract]

Restructurings

RESTRUCTURINGS

The restructuring charges that we expect to incur in connection with our restructurings are subject to a number of assumptions, and actual results may materially differ. We may also incur other material charges not currently contemplated due to events that may occur as a result of, or associated with, the restructurings.

2014 Restructuring

On September 2, 2014, we initiated a restructuring plan (the “2014 Restructuring”) to reduce our workforce and made personnel reductions across our entire organization. As a result of the 2014 Restructuring, we currently expect our workforce to reduce by approximately 65%, or approximately 150 employees, resulting in approximately 80 remaining employees. Personnel reductions were made across our entire organization. The 2014 Restructuring is a consequence of the failure of COMET-1, one of our two phase 3 pivotal trials of cabozantinib in metastatic castration-resistant prostate cancer, to meet its primary endpoint of demonstrating a statistically significant increase in overall survival for patients treated with cabozantinib as compared to prednisone. The principal objective of the 2014 Restructuring is to enable us to focus our financial resources on the phase 3 pivotal trials of cabozantinib in metastatic RCC and advanced HCC.

We expect to record an aggregate restructuring charge related to one-time termination benefits in the range of $6 million to $7 million, of which approximately 95% is expected in 2014 and the remainder is expected in the first quarter of 2015. We expect to incur additional charges as a result of the 2014 Restructuring, including facility-related charges, property and equipment write-downs and other charges, and expect to record the majority of these expenses during fiscal year 2014 as they become determinable and as we exit certain facilities. Except for employee severance and other benefits, we are currently unable to estimate the total amount or range of amounts expected to be incurred in connection with the 2014 Restructuring for each major type of cost or in the aggregate.

We have recorded a $3.3 million restructuring charge for the 2014 Restructuring during the three months ended September 30, 2014. The restructuring charge includes $2.6 million of employee severance and other benefits that are recognized ratably during the period from the implementation date of the 2014 Restructuring through the employees’ termination dates. In addition, we recorded $0.7 million of property and equipment write-downs. The total restructuring liability related to the 2014 Restructuring is included in the current portion of restructuring on the accompanying Consolidated Balance Sheets. The components and changes of these liabilities since initiation of the plan are summarized in the following table (in thousands):



	Employee Severance and Other Benefits			Asset Impairment and Other			Total
Restructuring charge	$	2,591		$	717		$	3,308
Cash payments	(62		)	—			(62		)
Adjustments or non-cash credits	22			(667		)	(645		)
Restructuring liability for 2014 Restructuring as of September 30, 2014	$	2,551		$	50		$	2,601

2010 Restructurings

Between March 2010 and May 2013, we implemented five restructurings (referred to collectively as the “2010 Restructurings”) to manage costs and as a consequence of our decision in 2010 to focus our proprietary resources and development efforts on the development and commercialization of cabozantinib. The aggregate reduction in headcount from the 2010 Restructurings was 429 employees. Charges and credits related to the 2010 Restructurings were recorded in periods other than those in which the 2010 Restructurings were implemented as a result of sublease activities for certain of our buildings in South San Francisco, California, changes in assumptions regarding anticipated sublease activities, the effect of the passage of time on our discounted cash flow computations, previously planned employee terminations, and sales of excess equipment and other assets.

For the nine months ended September 30, 2014 and 2013, we recorded restructuring charges of $0.8 million and $0.8 million, respectively for the 2010 Restructurings. The charges for both periods presented were related to the effect of the passage of time on our discounted cash flow computations for the exit, in prior periods, of certain of our South San Francisco buildings. During the nine months ended September 30, 2014, those charges were partially offset by $0.1 million in recoveries recorded in connection with the sale of excess equipment and other assets. The total outstanding restructuring liability related to the 2010 Restructurings is included in the current and long-term portion of restructuring on the accompanying Consolidated Balance Sheets. The components and changes of these liabilities during the nine months ended September 30, 2014 are summarized in the following table (in thousands):



	Facility Charges			Other			Total
Restructuring liability as of December 31, 2013	$	13,460		$	12		$	13,472
Restructuring charge (credit)	940			(113		)	827
Cash payments	(4,914		)	(6		)	(4,920		)
Adjustments or non-cash credits	8			(86		)	(78		)
Proceeds from sale of assets	—			199			199
Restructuring liability for 2010 Restructurings as of September 30, 2014	$	9,494		$	6		$	9,500

We expect to pay accrued facility charges of $9.5 million, net of cash received from our subtenants, through the end of our lease terms of the buildings, the last of which ends in 2017. We expect to incur additional restructuring charges of approximately $0.9 million relating to the effect of the passage of time on our discounted cash flow computations used to determine the accrued facilities charges through the end of the building lease terms.

Cash and Investments

9 Months Ended

Sep. 30, 2014

Investments, Debt and Equity Securities [Abstract]

Cash and Investments

CASH AND INVESTMENTS

The following table summarizes cash and cash equivalents, investments, and restricted cash and investments by balance sheet line item as of September 30, 2014 and December 31, 2013 (in thousands):



	September 30, 2014
	Amortized Cost		Gross Unrealized Gains		Gross Unrealized Losses			Fair Value
Cash and cash equivalents	$	100,065	$	—	$	—		$	100,065
Short-term investments	91,898		88		(49		)	91,937
Short-term restricted cash and investments	12,105		105		—			12,210
Long-term investments	84,601		20		(32		)	84,589
Long-term restricted cash and investments	4,684		—		—			4,684
Total cash and investments	$	293,353	$	213	$	(81	)	$	293,485



	December 31, 2013
	Amortized Cost		Gross Unrealized Gains		Gross Unrealized Losses			Fair Value
Cash and cash equivalents	$	103,978	$	—	$	—		$	103,978
Short-term investments	138,403		94		(22		)	138,475
Short-term restricted cash and investments	12,173		40		—			12,213
Long-term investments	144,226		106		(33		)	144,299
Long-term restricted cash and investments	16,837		60		—			16,897
Total cash and investments	$	415,617	$	300	$	(55	)	$	415,862

Under our loan and security agreement with Silicon Valley Bank, we are required to maintain compensating balances on deposit in one or more investment accounts with Silicon Valley Bank or one of its affiliates. The total collateral balances as of September 30, 2014 and December 31, 2013 were $82.4 million and $83.7 million, respectively, and are reflected on the accompanying Consolidated Balance Sheets in short- and long-term investments. See “Note 8 - Debt” to our Consolidated Financial Statements included in our Annual Report on Form 10-K for the year ended December 31, 2013, for more information regarding the collateral balance requirements under our Silicon Valley Bank loan and security agreement.

All of our cash equivalents and investments are classified as available-for-sale. The following table summarizes our cash equivalents and investments by security type as of September 30, 2014 and December 31, 2013. The amounts presented exclude cash, but include investments classified as cash equivalents (in thousands):



	September 30, 2014
	Amortized Cost		Gross Unrealized Gains		Gross Unrealized Losses			Fair Value
Money market funds	$	41,853	$	—	$	—		$	41,853
Commercial paper	72,346		—		—			72,346
Corporate bonds	155,078		101		(81		)	155,098
U.S. Treasury and government sponsored enterprises	12,105		105		—			12,210
Municipal bonds	8,229		7		—			8,236
Total investments	$	289,611	$	213	$	(81	)	$	289,743



	December 31, 2013
	Amortized Cost		Gross Unrealized Gains		Gross Unrealized Losses			Fair Value
Money market funds	$	24,813	$	—	$	—		$	24,813
Commercial paper	94,682		—		—			94,682
Corporate bonds	239,937		190		(55		)	240,072
U.S. Treasury and government sponsored enterprises	44,284		102		—			44,386
Municipal bonds	6,005		8					6,013
Total investments	$	409,721	$	300	$	(55	)	$	409,966

There were no realized gains or losses on the sales of investments during the nine months ended September 30, 2014 and 2013.

All of our investments are subject to a quarterly impairment review. During the nine months ended September 30, 2014 and 2013, we did not record any other-than-temporary impairment charges on our available-for-sale securities. As of September 30, 2014, there were 35 investments in an unrealized loss position with an aggregate fair value $64.6 million. The investments in an unrealized loss position consist solely of corporate bonds. All of our investments in an unrealized loss position have been so for less than one year and the unrealized losses were not attributed to credit risk, but rather associated with the changes in interest rates. Based on the scheduled maturities of our investments, 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 the fair value of securities classified as available-for-sale by contractual maturity as of September 30, 2014 (in thousands):



	Mature within One Year		After One Year through Two Years		Fair Value
Money market funds	$	41,853	$	—	$	41,853
Commercial paper	72,346		—		72,346
Corporate bonds	133,306		21,792		155,098
U.S. Treasury and government sponsored enterprises	12,210		—		12,210
Municipal bonds	8,236		—		8,236
Total investments	$	267,951	$	21,792	$	289,743

Cash is excluded from the table above. The classification of certain compensating balances and restricted investments are dependent upon the term of the underlying restriction on the asset and not the maturity date of the investment. Therefore, certain long-term investments and long-term restricted cash and investments have contractual maturities within one year.

Inventory

9 Months Ended

Sep. 30, 2014

Inventory Disclosure [Abstract]

Inventory

INVENTORY

Inventory consists of the following (in thousands):



	September 30, 2014		December 31, 2013
Raw materials	$	787	$	529
Work in process	2,501		2,280
Finished goods	588		81
Total	$	3,876	$	2,890

We received regulatory approval in the United States for our first product, COMETRIQ, on November 29, 2012. A significant portion of the manufacturing costs for our inventory were incurred prior to regulatory approval of COMETRIQ for the treatment of progressive, metastatic MTC and, therefore, were expensed as research and development costs when those costs were incurred, rather than capitalized as inventory.

Debt

9 Months Ended

Sep. 30, 2014

Debt Disclosure [Abstract]

Debt

DEBT

The amortized carrying amount of our debt consists of the following (in thousands):



	September 30, 2014			December 31, 2013
Convertible Senior Subordinated Notes due 2019	$	177,962		$	165,296
Secured Convertible Notes due 2015	96,496			99,851
Silicon Valley Bank term loan	80,000			80,000
Silicon Valley Bank line of credit	757			2,090
Total debt	355,215			347,237
Less: current portion	(97,253		)	(11,762		)
Long-term debt	$	257,962		$	335,475

See “Note 8 - Debt” to our Consolidated Financial Statements included in our Annual Report on Form 10-K for the year ended December 31, 2013, for additional information on the terms of our debt, including a description of the conversion features of the of 4.25% Convertible Senior Subordinated Notes due 2019 (the “2019 Notes”) and our Secured Convertible Notes due June 2015 (the “Deerfield Notes”).

Convertible Senior Subordinated Notes due 2019

In August 2012, we issued and sold $287.5 million aggregate principal amount of the 2019 Notes. As of September 30, 2014, the entire principal balance remains outstanding. The following is a summary of the liability component of the 2019 Notes (in thousands):



	September 30, 2014		December 31, 2013
Net carrying amount of the liability component	$	177,962	$	165,296
Unamortized discount of the liability component	109,538		122,204
Face amount of the 2019 Notes	$	287,500	$	287,500

The debt discount and debt issuance costs will be amortized as interest expense through August 2019. The following is a summary of interest expense for the 2019 Notes (in thousands):



	Three Months Ended September 30,				Nine Months Ended September 30,
	2014		2013		2014		2013
Stated coupon interest	$	3,055	$	3,055	$	9,198	$	9,164
Amortization of debt discount and debt issuance costs	4,502		4,097		13,194		12,007
Total interest expense	$	7,557	$	7,152	$	22,392	$	21,171

The balance of unamortized fees and costs was $3.4 million and $4.0 million as of September 30, 2014 and December 31, 2013, respectively, which is included in Other assets on the accompanying Consolidated Balance Sheets.

Secured Convertible Notes due June 2015

In June 2010, we entered into a note purchase agreement with entities affiliated with Deerfield Management Company, L.P. (“Deerfield”), pursuant to which, on July 1, 2010, we sold to Deerfield an aggregate of $124.0 million in principal amount of the Deerfield Notes. As of September 30, 2014 and December 31, 2013, the remaining outstanding principal balance on the Deerfield Notes was $104.0 million and $114.0 million, respectively, which, subject to certain limitations, is payable in cash or in stock at our discretion. The following is a summary of interest expense for the Deerfield Notes (in thousands):



	Three Months Ended September 30,				Nine Months Ended September 30,
	2014		2013		2014		2013
Stated coupon interest	$	1,512	$	1,513	$	4,487	$	4,488
Amortization of debt discount and debt issuance costs	3,005		2,555		8,631		7,438
Total interest expense	$	4,517	$	4,068	$	13,118	$	11,926

The balance of unamortized fees and costs was $2.1 million and $1.4 million as of September 30, 2014 and December 31, 2013, respectively, which is included in Other assets on the accompanying Consolidated Balance Sheets.

On January 22, 2014, the note purchase agreement was amended to provide us with an option to extend the maturity date of our indebtedness under the note purchase agreement to July 1, 2018 (the “Extension Option”). Under the terms of the Extension Option, which expires on March 31, 2015, we have the right to require Deerfield Partners, L.P. and Deerfield International Master Fund, L.P. (the “New Deerfield Purchasers”) to acquire $100 million principal amount of the Deerfield Notes and extend the maturity date to July 1, 2018. If we exercise the Extension Option, the Deerfield Notes would bear interest on and after July 2, 2015 at the rate of 7.5% per annum to be paid in cash, quarterly in arrears, and 7.5% per annum to be paid in kind, quarterly in arrears, for a total interest rate of 15% per annum. We are under no obligation to exercise the Extension Option.

In connection with the amendment to the note purchase agreement, on January 22, 2014 we issued to the New Deerfield Purchasers two-year warrants (the “2014 Deerfield Warrants”) to purchase an aggregate of 1,000,000 shares of our common stock at an exercise price of $9.70 per share, which exercise price is subject to change in the event we exercise the Extension Option. See “Note 6 - Common Stock and Warrants” for further information on those warrants.

We determined that the amendment resulted in the Deerfield Notes being modified. In connection with the amendment, we recorded a $2.8 million deferred commitment fee upon the issuance of the 2014 Deerfield Warrants. See “Note 6 - Common Stock and Warrants” for further information on those warrants. The deferred commitment fee is included in Other assets and will be amortized into interest expense as a yield adjustment through the current maturity date of the Deerfield Notes, July 1, 2015. Third-party expenses, comprised primarily of legal and accounting fees, were expensed as of the date of the amendment.

Common Stock And Warrants

9 Months Ended

Sep. 30, 2014

Warrants and Rights Note Disclosure [Abstract]

Common Stock And Warrants

COMMON STOCK AND WARRANTS

Sale of Shares of Common Stock

In January 2014, we completed a registered underwritten public offering of 10.0 million shares of our common stock at a price of $8.00 per share pursuant to a shelf registration statement previously filed with the SEC, which the SEC declared effective on June 8, 2012. We received $75.6 million in net proceeds from the offering after deducting the underwriting discount and related offering expenses.

Warrants

On January 22, 2014, in connection with the amendment to the note purchase agreement to provide us with the Extension Option, we issued to the New Deerfield Purchasers the 2014 Deerfield Warrants to purchase an aggregate of 1,000,000 shares of our common stock at an exercise price of $9.70 per share. If we exercise the Extension Option, the term of the 2014 Deerfield Warrants will be extended by two years and the exercise price will be reset to the lower of (i) the existing exercise price and (ii) 120% of the volume weighted average price of our common stock for the ten trading days immediately following the date of such extension election. Due to the potential increase in term and decrease of the exercise price, the 2014 Deerfield Warrants were recorded as a liability which is included in Other long-term liabilities. The 2014 Deerfield Warrants are recorded at fair value, on a recurring basis, which was $0.8 million and $2.8 million as of September 30, 2014 and January 22, 2014, respectively. We recorded an unrealized gain on the warrants of $0.1 million and $1.9 million during the three and nine months ended September 30, 2014, respectively, which is included in Interest income and other, net. See “Note 7 - Fair Value Measurements” for more information on the valuation of these warrants.

At September 30, 2014, the following warrants to purchase common stock were outstanding and exercisable:



Date Issued	Exercise Price per Share		Expiration Date	Number of Shares
January 22, 2014	$	9.70	January 22, 2016	1,000,000

The warrants are participating securities. The warrant holders do not have a contractual obligation to share in our losses.

Fair Value Measurements

9 Months Ended

Sep. 30, 2014

Fair Value Disclosures [Abstract]

Fair Value Measurements

FAIR VALUE MEASUREMENTS

The following table sets forth the fair value of our financial assets and liabilities that were measured and recorded on a recurring basis as of September 30, 2014 and December 31, 2013. We did not have any financial liabilities that were measured and recorded on a recurring basis or Level 3 investments as of December 31, 2013. The amounts presented exclude cash, but include investments classified as cash equivalents (in thousands):



	September 30, 2014
	Level 1		Level 2		Level 3		Total
Financial assets:
Money market funds	$	41,853	$	—	$	—	$	41,853
Commercial paper	—		72,346		—		72,346
Corporate bonds	—		155,098		—		155,098
U.S. Treasury and government sponsored enterprises	—		12,210		—		12,210
Municipal bonds	—		8,236		—		8,236
Total financial assets	$	41,853	$	247,890	$	—	$	289,743
Financial liabilities:
Warrants	$	—	$	—	$	846	$	846
Total financial liabilities	$	—	$	—	$	846	$	846



	December 31, 2013
	Level 1		Level 2		Total
Money market funds	$	24,813	$	—	$	24,813
Commercial paper	—		94,682		94,682
Corporate bonds	—		240,072		240,072
U.S. Treasury and government sponsored enterprises	—		44,386		44,386
Municipal bonds	—		6,013		6,013
Total financial assets	$	24,813	$	385,153	$	409,966

There were no transfers between any of the fair value hierarchies, as determined at the end of each reporting period.

The estimated fair values of our financial instruments that are carried at amortized cost for which it is practicable to determine a fair value were as follows (in thousands):



	September 30, 2014				December 31, 2013
	Carrying Amount		Fair Value		Carrying Amount		Fair Value
2019 Notes	$	177,962	$	159,850	$	165,296	$	339,883
Silicon Valley Bank term loan	$	80,000	$	79,958	$	80,000	$	79,946
Silicon Valley Bank line of credit	$	757	$	757	$	2,090	$	2,090

We believe it is not practicable to determine the fair value of the Deerfield Notes due to the unique structure of the instrument that was financed by entities affiliated with Deerfield.

The carrying amounts of cash, trade and other receivables, accounts payable and accrued clinical trial liabilities approximate their fair values and are excluded from the tables above.

The following methods and assumptions were used to estimate the fair value of each class of financial instrument for which it is practicable to estimate a value:


•	When available, we value investments based on quoted prices for those financial instruments, which is a Level 1 input. Our remaining investments are valued using third-party pricing sources, which use observable market prices, interest rates and yield curves observable at commonly quoted intervals of similar assets as observable inputs for pricing, which is a Level 2 input.


•	The 2019 Notes are valued using a third-party pricing model that is based in part on average trading prices, which is a Level 2 input. The 2019 Notes are not marked-to-market and are shown at their initial fair value less the unamortized discount; the portion of the value allocated to the conversion option is included in Stockholders’ equity on the accompanying Consolidated Balance Sheets.


•	We estimate the fair value of our other 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.

•

The 2014 Deerfield Warrants are valued using a Monte Carlo simulation model. The expected life is based on the contractual terms of the 2014 Deerfield Warrants, and in certain simulations, assumes the two year extension that would result from our exercise of the Extension Option; as of September 30, 2014, we have estimated that is it probable that we will exercise this two-year extension. We consider implied volatility as well as our historical volatility in developing our estimate of expected volatility. The fair value of the 2014 Deerfield Warrants were estimated using the following assumptions, which, except for risk-free interest rate, are Level 3 inputs (dollars in thousands):



	September 30, 2014			January 22, 2014 (issuance date)
Fair value of warrants	$	846		$	2,762
Risk-free interest rate	0.99		%	0.95		%
Dividend yield	—		%	—		%
Volatility	95		%	57		%
Average expected life	3.3 years			3.2 years

- Definition

The entire disclosure for the fair value of financial instruments (as defined), including financial assets and financial liabilities (collectively, as defined), and the measurements of those instruments as well as disclosures related to the fair value of non-financial assets and liabilities. Such disclosures about the financial instruments, assets, and liabilities would include: (1) the fair value of the required items together with their carrying amounts (as appropriate); (2) for items for which it is not practicable to estimate fair value, disclosure would include: (a) information pertinent to estimating fair value (including, carrying amount, effective interest rate, and maturity, and (b) the reasons why it is not practicable to estimate fair value; (3) significant concentrations of credit risk including: (a) information about the activity, region, or economic characteristics identifying a concentration, (b) the maximum amount of loss the entity is exposed to based on the gross fair value of the related item, (c) policy for requiring collateral or other security and information as to accessing such collateral or security, and (d) the nature and brief description of such collateral or security; (4) quantitative information about market risks and how such risks are managed; (5) for items measured on both a recurring and nonrecurring basis information regarding the inputs used to develop the fair value measurement; and (6) for items presented in the financial statement for which fair value measurement is elected: (a) information necessary to understand the reasons for the election, (b) discussion of the effect of fair value changes on earnings, (c) a description of [similar groups] items for which the election is made and the relation thereof to the balance sheet, the aggregate carrying value of items included in the balance sheet that are not eligible for the election; (7) all other required (as defined) and desired information.

+ References + Details

Stock-Based Compensation

9 Months Ended

Sep. 30, 2014

Share-based Compensation [Abstract]

Stock-Based Compensation

STOCK-BASED COMPENSATION

We recorded and allocated employee stock-based compensation expenses for our equity incentive plans and our 2000 Employee Stock Purchase Plan (“ESPP”) as follows (in thousands):



	Three Months Ended September 30,					Nine Months Ended September 30,
	2014			2013		2014			2013
Research and development expense	$	112		$	1,415	$	3,148		$	4,326
Selling, general and administrative expense	624			1,478		5,328			4,115
Restructuring-related stock-based compensation (recovery) expense	(22		)	—		(22		)	49
Total employee stock-based compensation expense	$	714		$	2,893	$	8,454		$	8,490

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 stock option awards and ESPP purchases was estimated using the following assumptions and weighted average fair values:



	Stock Options
	Three Months Ended September 30,						Nine Months Ended September 30,
	2014			2013			2014			2013
Weighted average grant-date fair value	$	1.19		$	2.99		$	1.47		$	2.92
Risk-free interest rate	1.83		%	1.57		%	1.81		%	1.47		%
Dividend yield	—		%	—		%	—		%	—		%
Volatility	86		%	60		%	85		%	60		%
Expected life	5.5 years			5.6 years			5.5 years			5.6 years



	Employee Stock Purchase Plan
	Three Months Ended September 30,						Nine Months Ended September 30,
	2014			2013			2014			2013
Weighted average grant-date fair value	$	1.21		$	1.74		$	1.35		$	1.66
Risk-free interest rate	0.05		%	0.08		%	0.06		%	0.12		%
Dividend yield	—		%	—		%	—		%	—		%
Volatility	68		%	67		%	66		%	67		%
Expected life	6 months			6 months			6 months			6 months

Of the stock options outstanding as of September 30, 2014, options with respect to 11,359,106 shares were granted subject to performance objectives tied to the achievement of goals set by the Compensation Committee of our Board of Directors and will vest in full or in part based on achievement of such goals. We do not record any stock-based compensation expense for stock options with performance objectives for which the achievement of the goals is not considered probable; as of September 30, 2014, the grant date fair value of awards outstanding for which we have determined that it is not probable that we will achieve the goals was $19.0 million. As a consequence of the failure of COMET-1, we determined that achievement of certain performance objectives previously considered to be probable were no longer probable; as a result, during the three months ended September 30, 2014, we reversed $2.1 million of previously recorded stock-based compensation expense in connection with such awards and cancelled 692,896 stock options with performance objectives which could no longer be achieved; if COMET-2 meets its primary endpoint, we will record $1.1 million in stock-based compensation for those stock options in the period those trial results are determined.

A summary of all stock option activity for the nine months ended September 30, 2014 is presented below (dollars in thousands, except per share amounts):



	Shares		Weighted Average Exercise Price		Weighted Average Remaining Contractual Term	Aggregate Intrinsic Value
Options outstanding at December 31, 2013	23,983,275		$	6.48
Granted	9,653,615		$	2.13
Exercised	(19,090	)	$	6.28
Forfeited	(882,864	)	$	5.53
Expired	(669,778	)	$	7.31
Options outstanding at September 30, 2014	32,065,158		$	5.18	4.81 years	$	—
Exercisable September 30, 2014	15,478,788		$	6.93	3.21 years	$	—

As of September 30, 2014, $28.3 million of total unrecognized compensation expense related to employee stock options was expected to be recognized over a weighted-average period of 2.70 years.

A summary of all restricted stock unit (“RSU”) activity for the nine months ended September 30, 2014 is presented below (dollars in thousands, except per share amounts):



	Shares		Weighted Average Grant Date Fair Value		Weighted Average Remaining Contractual Term	Aggregate Intrinsic Value
Awards outstanding at December 31, 2013	1,810,521		$	5.56
Awarded	64,637		$	5.11
Released	(114,704	)	$	6.68
Forfeited	(98,073	)	$	5.44
Awards outstanding at September 30, 2014	1,662,381		$	5.48	2.72 years	$	2,593

As of September 30, 2014, $2.0 million of total unrecognized compensation expense related to employee RSUs was expected to be recognized over a weighted-average period of 2.72 years.

Net Loss Per Share

9 Months Ended

Sep. 30, 2014

Earnings Per Share [Abstract]

Net Loss Per Share

NET LOSS PER SHARE

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



	Three Months Ended September 30,						Nine Months Ended September 30,
	2014			2013			2014			2013
Numerator:
Net loss	$	(62,560	)	$	(67,124	)	$	(210,589	)	$	(174,014	)
Denominator:
Shares used in computing basic and diluted net loss per share	195,126			184,149			193,855			183,957
Net loss per share, basic and diluted	$	(0.32	)	$	(0.36	)	$	(1.09	)	$	(0.95	)

The following table sets forth outstanding potentially dilutive shares of common stock that are not included in the computation of diluted net loss per share because, to do so would be anti-dilutive (in thousands):



	September 30
	2014	2013
Convertible debt	75,734	54,123
Outstanding stock options, unvested RSUs and ESPP contributions	34,243	25,694
Warrants	1,000	1,441
Total potentially dilutive shares	110,977	81,258

Concentrations of Credit Risk

9 Months Ended

Sep. 30, 2014

Risks and Uncertainties [Abstract]

Concentrations of Credit Risk

CONCENTRATIONS OF CREDIT RISK

Financial instruments that potentially subject us to concentrations of credit risk are primarily trade and other receivables and investments. Investments consist of money market funds, taxable commercial paper, corporate bonds with high credit quality, U.S. Treasury and government sponsored enterprises, and municipal bonds. All investments are maintained with financial institutions that management believes are creditworthy.

Trade and other receivables are 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. As of September 30, 2014, 74% of our trade and other receivables are with the specialty pharmacy that sells COMETRIQ in the United States and 15% are with our European distribution partner. Both of these customers pay promptly and within their respective payment terms. All of our long-lived assets are located in the United States.

We have operations primarily in the United States, while some of our collaboration partners have headquarters outside of the United States and some of our clinical trials for cabozantinib are conducted outside of the United States. During the second quarter of 2013, we initiated a Named Patient Use (“NPU”) program through our distribution partner, Swedish Orphan Biovitrum (“Sobi”), to support the distribution and commercialization of COMETRIQ for metastatic MTC primarily in the European Union and potentially other countries. In March 2014, the European Commission approved cabozantinib for the treatment of adult patients with progressive, unresectable locally advanced or metastatic MTC, also under the brand name COMETRIQ. In June 2014, we began selling COMETRIQ to Sobi in preparation for commercial sales in certain countries in the European Union. The following table shows the percentage of revenues earned in the United States and the European Union.



	Three Months Ended September 30,				Nine Months Ended September 30,
	2014		2013		2014		2013
Percentage of revenues earned in the United States	108	%	87	%	100	%	96	%
Percentage of revenues earned in the European Union	(8	)%	13	%	—	%	4	%

Net product revenues in the European Union for the three months ended September 30, 2014 included a $1.8 million reduction to revenue for a project management fee payable to our European distributor upon their achievement of a cumulative revenue goal. As a result, for the three months ended September 30, 2014 discounts and allowances exceeded gross revenues for the European Union causing the percentage of revenues earned in the United States to exceed 100% during the period.

The following table sets forth the percentage of revenues recognized under our collaboration agreements and product sales to the specialty pharmacy that represent 10% or more of total revenues during the three and nine months ended September 30, 2014 and 2013:



	Three Months Ended September 30,				Nine Months Ended September 30,
	2014		2013		2014		2013
Collaboration agreement:
Bristol-Myers Squibb	—	%	13	%	—	%	60	%
Product sales:
Diplomat Specialty Pharmacy	108	%	74	%	100	%	36	%

Disposition of Artemis Pharmaceuticals	9 Months Ended
Disposition of Artemis Pharmaceuticals	Sep. 30, 2014
Discontinued Operations and Disposal Groups [Abstract]
Disposition of Artemis Pharmaceuticals	DISPOSITION OF ARTEMIS PHARMACEUTICALS In November 2007, we entered into a share sale and transfer agreement with Taconic Farms, Inc., (“Taconic”), pursuant to which Taconic acquired from us, 80.1% of the outstanding share capital in our wholly-owned subsidiary, Artemis Pharmaceuticals GmbH (“Artemis”). In September 2011, we exercised our right to sell our remaining 19.9% interest in Artemis to Taconic. In September 2014, we received an $0.8 million purchase price adjustment resulting from the resolution of contingencies from the September 2011 sale of our remaining interest in Artemis to Taconic. This $0.8 million gain on sale of a business is included in interest income and other, net on our Condensed Consolidated Statements of Operations.

- Definition

The entire disclosure for the facts and circumstances leading to the completed or expected disposal, manner and timing of disposal, the gain (loss) recognized in the income statement and the income statement caption that includes that gain (loss), amounts of revenues and pretax profit or loss reported in discontinued operations, the segment in which the disposal group was reported, and the classification (whether sold or classified as held for sale) and carrying value of the assets and liabilities comprising the disposal group. Includes all disposal groups, including those classified as components of the entity (discontinued operations).

+ References

Reference 1: http://www.xbrl.org/2003/role/presentationRef
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-Name Accounting Standards Codification
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Reference 6: http://www.xbrl.org/2003/role/presentationRef
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Reference 7: http://www.xbrl.org/2003/role/presentationRef
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+ Details

Organization and Summary of Significant Accounting Policies (Policies)	9 Months Ended
	Sep. 30, 2014
Organization, Consolidation and Presentation of Financial Statements [Abstract]
Organization	Organization Exelixis, Inc. (“Exelixis,” “we,” “our” or “us”) is a biopharmaceutical company committed to developing small molecule therapies for the treatment of cancer. Our two most advanced assets are cabozantinib, our wholly-owned inhibitor of multiple receptor tyrosine kinases, and cobimetinib (GDC-0973/XL518), a potent, highly selective inhibitor of MEK, which we out-licensed to Genentech (a member of the Roche Group) (“Genentech”). We are focusing our development and commercialization efforts primarily on cabozantinib. We are evaluating cabozantinib in a broad development program comprising over forty-five clinical trials, including three ongoing phase 3 pivotal trials across multiple indications, with particular focus on our phase 3 pivotal trials in metastatic renal cell carcinoma (“RCC”) and advanced hepatocellular carcinoma (“HCC”). Cabozantinib was approved by the United States Food and Drug Administration (“FDA”) on November 29, 2012 for the treatment of progressive, metastatic medullary thyroid cancer (“MTC”) in the United States under the brand name COMETRIQ^(R). COMETRIQ became commercially available in the United States in late January 2013. In March 2014, the European Commission approved cabozantinib for the treatment of adult patients with progressive, unresectable locally advanced or metastatic MTC, also under the brand name COMETRIQ. The European Commission granted conditional marketing authorization following a positive opinion from the European Committee for Medicinal Products for Human Use, issued in December 2013. Our second oncology asset, cobimetinib, is being evaluated by Genentech in a broad development program, including coBRIM, a phase 3 pivotal trial evaluating cobimetinib in combination with vemurafenib in previously untreated patients with unresectable locally advanced or metastatic melanoma harboring a BRAF^V600 mutation. On September 29, 2014, positive results from this trial were reported at the European Society for Medical Oncology 2014 Congress. The trial met its primary endpoint of demonstrating a statistically significant increase in investigator-determined progression-free survival. Roche has completed the Marketing Authorization Application for the combination of cobimetinib and vemurafenib in the European Union. In the United States, cobimetinib has received Fast Track Designation from the FDA, and Genentech expects to complete its New Drug Application filing for the combination before the end of this year.
Basis of Consolidation	Basis of Consolidation The consolidated financial statements include the accounts of Exelixis and those of our wholly-owned subsidiaries. These entities’ functional currency is the U.S. dollar. All intercompany balances and transactions have been eliminated.
Basis of Presentation	Basis of Presentation The accompanying unaudited 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 for complete financial statements. In our opinion, all adjustments (consisting only 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 generally ends on the Friday closest to December 31st. Fiscal year 2013, a 52-week year, ended on December 27, 2013, and fiscal year 2014, a 53-week year, will end on January 2, 2015. For convenience, references in this report as of and for the fiscal periods ended September 26, 2014 and September 27, 2013, and as of the fiscal year ended December 27, 2013, are indicated as ended September 30, 2014, September 30, 2013, and December 31, 2013, respectively. Operating results for the nine months ended September 30, 2014 are not necessarily indicative of the results that may be expected for the fiscal year ending January 2, 2015 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 year ended December 31, 2013, included in our Annual Report on Form 10-K filed with the SEC on February 20, 2014.
Fiscal Period, Policy	Exelixis adopted a 52- or 53-week fiscal year that generally ends on the Friday closest to December 31st. Fiscal year 2013, a 52-week year, ended on December 27, 2013, and fiscal year 2014, a 53-week year, will end on January 2, 2015. For convenience, references in this report as of and for the fiscal periods ended September 26, 2014 and September 27, 2013, and as of the fiscal year ended December 27, 2013, are indicated as ended September 30, 2014, September 30, 2013, and December 31, 2013, respectively.
Segment Information	Segment Information We operate as a single reportable segment.
Use of Estimates	Use of Estimates The preparation of our consolidated financial statements is in conformity with accounting principles generally accepted in the United States which requires management to make judgments, 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 inventory, revenue recognition, valuation of long-lived assets, certain accrued liabilities including clinical trial accruals and restructuring liability, valuation of warrants, share-based compensation and the valuation of the debt and equity components of our convertible debt at issuance. We base our estimates on historical experience and on various other market-specific and other relevant assumptions that we believe 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.
Revenue Recognition	Revenue Recognition We recognize revenue from the sale of COMETRIQ and from license fees and milestones earned on research and collaboration arrangements. See “Note 1 - Organization and Summary of Significant Accounting Policies” to our Consolidated Financial Statements included in our Annual Report on Form 10-K for the year ended December 31, 2013 for a description of our policies for revenue recognition on research and collaboration agreements. We did not enter into any new collaboration agreements during the nine months ended September 30, 2014. See “Note 2 - Research and Collaboration Agreements” to our Consolidated Financial Statements included in our Annual Report on Form 10-K for the year ended December 31, 2013 for a description of our existing collaboration agreements. Net Product Revenues We recognize revenue when it is both realized or realizable and earned, meaning persuasive evidence of an arrangement exists, delivery has occurred, title has transferred, the price is fixed or determinable, there are no remaining customer acceptance requirements, and collectability of the resulting receivable is reasonably assured. For product sales in the United States, this generally occurs upon shipment of the product to the patient by our distributor. For product sales in Europe, this occurs when our European distribution partner has accepted the product. We sell our product, COMETRIQ, in the United States to a specialty pharmacy that benefits from customer incentives and has a right of return. We have a limited sales history and cannot reliably estimate expected returns of the product nor the discounts and rebates due to payors at the time of shipment to the specialty pharmacy. Accordingly, upon shipment to the specialty pharmacy, we record deferred revenue on our Consolidated Balance Sheets. We recognize revenue when the specialty pharmacy provides the product to a patient based on the fulfillment of a prescription. We record revenue using an analysis of prescription data from our specialty pharmacy to ascertain the date of shipment and the payor mix. This approach is frequently referred to as the “sell-through” revenue recognition model. Once the prescription has been provided to the patient, it is not subject to return unless the product is damaged. We record revenue at the time our European distribution partner has accepted the product, a method also known as the “sell-in” revenue recognition model. Product Sales Discounts and Allowances We calculate gross product revenues based on the price that we charge our United States specialty pharmacy and our European distribution partner. We estimate our domestic net product revenues by deducting from our gross product revenues (a) trade allowances, such as discounts for prompt payment, (b) estimated government rebates and chargebacks, and (c) estimated costs of patient assistance programs. We initially record estimates for these deductions at the time we recognize the gross revenue. We update our estimates on a recurring basis as new information becomes available. See “Note 1 - Organization and Summary of Significant Accounting Policies” to our Consolidated Financial Statements included in our Annual Report on Form 10-K for the year ended December 31, 2013 for a further description of our discounts and allowances. Our European distribution partner is entitled to receive a project management fee based upon the achievement of a pre-specified revenue goal which, when deemed probable, is ratably accrued as a reduction to gross revenue.
Cost of Goods Sold	Cost of Goods Sold Cost of goods sold is related to our product revenues and consists primarily of a 3% royalty and indirect labor costs, and to a lesser extent, the cost of manufacturing and other third party logistics costs of our product. A significant portion of the manufacturing costs for product sales were incurred prior to regulatory approval of COMETRIQ for the treatment of progressive, metastatic MTC and, therefore, were expensed as research and development costs when those costs were incurred, rather than capitalized as inventory. In accordance with our product development and commercialization agreement with GlaxoSmithKline, we are required to pay GlaxoSmithKline a 3% royalty on the Net Sales of any product incorporating cabozantinib, including COMETRIQ. Net Sales is defined in the product development and commercialization agreement generally as the gross invoiced sales price less customer credits, rebates, chargebacks, shipping costs, customs duties, and sales tax and other similar tax payments we are required to make.
Recently Issued Accounting Pronouncements	Recently Issued Accounting Pronouncements In May 2014, the Financial Accounting Standards Board (“FASB”) issued Accounting Standards Update (“ASU”) 2014-09, Revenue from Contracts with Customers (“ASU 2014-09”). ASU 2014-09 supersedes the revenue recognition requirements of FASB Accounting Standards Codification (“ASC”) Topic 605, Revenue Recognition and most industry-specific guidance throughout the Accounting Standards Codification, resulting in the creation of FASB ASC Topic 606, Revenue from Contracts with Customers. ASU 2014-09 requires entities to recognize revenue in a way that depicts the transfer of promised goods or services to customers in an amount that reflects the consideration to which the entity expects to be entitled to in exchange for those goods or services. Adoption will be permitted using either a retrospective or modified retrospective approach, and is effective for fiscal years, and interim periods within those years, beginning after December 15, 2016. Early adoption is not permitted. We are currently evaluating the impact of adopting this ASU, inclusive of available transitional methods on our consolidated financial statements and related disclosures. In August 2014, the FASB issued ASU 2014-15, Presentation of Financial Statements-Going Concern (“ASU 2014-15”). ASU 2014-15 provides guidance on management’s responsibility in evaluating whether there are conditions or events that raise substantial doubt about a company’s ability to continue as a going concern within one year from the date the financial statements are issued, and about related footnote disclosures. ASU 2014-15 is effective for the annual period ending after December 15, 2016, and for annual periods and interim periods thereafter. Early application is permitted. We are currently evaluating the impact of adopting ASU 2014-15 and its related disclosures.

Restructurings (Tables)

9 Months Ended

Sep. 30, 2014

2014 Restructuring [Member]

Restructuring Cost and Reserve [Line Items]

Summary Of Components Of Restructuring Liability

The components and changes of these liabilities since initiation of the plan are summarized in the following table (in thousands):



	Employee Severance and Other Benefits			Asset Impairment and Other			Total
Restructuring charge	$	2,591		$	717		$	3,308
Cash payments	(62		)	—			(62		)
Adjustments or non-cash credits	22			(667		)	(645		)
Restructuring liability for 2014 Restructuring as of September 30, 2014	$	2,551		$	50		$	2,601

2010 Restructurings [Member]

Restructuring Cost and Reserve [Line Items]

Summary Of Components Of Restructuring Liability

The components and changes of these liabilities during the nine months ended September 30, 2014 are summarized in the following table (in thousands):



	Facility Charges			Other			Total
Restructuring liability as of December 31, 2013	$	13,460		$	12		$	13,472
Restructuring charge (credit)	940			(113		)	827
Cash payments	(4,914		)	(6		)	(4,920		)
Adjustments or non-cash credits	8			(86		)	(78		)
Proceeds from sale of assets	—			199			199
Restructuring liability for 2010 Restructurings as of September 30, 2014	$	9,494		$	6		$	9,500

Cash and Investments Cash and Investments (Tables)

9 Months Ended

Sep. 30, 2014

Investments, Debt and Equity Securities [Abstract]

Schedule of Available-for-Sale Securities

The following table summarizes cash and cash equivalents, investments, and restricted cash and investments by balance sheet line item as of September 30, 2014 and December 31, 2013 (in thousands):



	September 30, 2014
	Amortized Cost		Gross Unrealized Gains		Gross Unrealized Losses			Fair Value
Cash and cash equivalents	$	100,065	$	—	$	—		$	100,065
Short-term investments	91,898		88		(49		)	91,937
Short-term restricted cash and investments	12,105		105		—			12,210
Long-term investments	84,601		20		(32		)	84,589
Long-term restricted cash and investments	4,684		—		—			4,684
Total cash and investments	$	293,353	$	213	$	(81	)	$	293,485



	December 31, 2013
	Amortized Cost		Gross Unrealized Gains		Gross Unrealized Losses			Fair Value
Cash and cash equivalents	$	103,978	$	—	$	—		$	103,978
Short-term investments	138,403		94		(22		)	138,475
Short-term restricted cash and investments	12,173		40		—			12,213
Long-term investments	144,226		106		(33		)	144,299
Long-term restricted cash and investments	16,837		60		—			16,897
Total cash and investments	$	415,617	$	300	$	(55	)	$	415,862

Summary of Cash and Investments by Security Type

The amounts presented exclude cash, but include investments classified as cash equivalents (in thousands):



	September 30, 2014
	Amortized Cost		Gross Unrealized Gains		Gross Unrealized Losses			Fair Value
Money market funds	$	41,853	$	—	$	—		$	41,853
Commercial paper	72,346		—		—			72,346
Corporate bonds	155,078		101		(81		)	155,098
U.S. Treasury and government sponsored enterprises	12,105		105		—			12,210
Municipal bonds	8,229		7		—			8,236
Total investments	$	289,611	$	213	$	(81	)	$	289,743



	December 31, 2013
	Amortized Cost		Gross Unrealized Gains		Gross Unrealized Losses			Fair Value
Money market funds	$	24,813	$	—	$	—		$	24,813
Commercial paper	94,682		—		—			94,682
Corporate bonds	239,937		190		(55		)	240,072
U.S. Treasury and government sponsored enterprises	44,284		102		—			44,386
Municipal bonds	6,005		8					6,013
Total investments	$	409,721	$	300	$	(55	)	$	409,966

Summary of Available-for-Sale Securities by Contractual Maturity

The following summarizes the fair value of securities classified as available-for-sale by contractual maturity as of September 30, 2014 (in thousands):



	Mature within One Year		After One Year through Two Years		Fair Value
Money market funds	$	41,853	$	—	$	41,853
Commercial paper	72,346		—		72,346
Corporate bonds	133,306		21,792		155,098
U.S. Treasury and government sponsored enterprises	12,210		—		12,210
Municipal bonds	8,236		—		8,236
Total investments	$	267,951	$	21,792	$	289,743

Inventory (Tables)

9 Months Ended

Sep. 30, 2014

Inventory Disclosure [Abstract]

Schedule of Inventory

Inventory consists of the following (in thousands):



	September 30, 2014		December 31, 2013
Raw materials	$	787	$	529
Work in process	2,501		2,280
Finished goods	588		81
Total	$	3,876	$	2,890

Debt (Tables)

9 Months Ended

Sep. 30, 2014

Debt Disclosure [Abstract]

Schedule Of Debt

The amortized carrying amount of our debt consists of the following (in thousands):



	September 30, 2014			December 31, 2013
Convertible Senior Subordinated Notes due 2019	$	177,962		$	165,296
Secured Convertible Notes due 2015	96,496			99,851
Silicon Valley Bank term loan	80,000			80,000
Silicon Valley Bank line of credit	757			2,090
Total debt	355,215			347,237
Less: current portion	(97,253		)	(11,762		)
Long-term debt	$	257,962		$	335,475

Summary Of The Liability Component Notes

The following is a summary of the liability component of the 2019 Notes (in thousands):



	September 30, 2014		December 31, 2013
Net carrying amount of the liability component	$	177,962	$	165,296
Unamortized discount of the liability component	109,538		122,204
Face amount of the 2019 Notes	$	287,500	$	287,500

The debt discount and debt issuance costs will be amortized as interest expense through August 2019. The following is a summary of interest expense for the 2019 Notes (in thousands):



	Three Months Ended September 30,				Nine Months Ended September 30,
	2014		2013		2014		2013
Stated coupon interest	$	3,055	$	3,055	$	9,198	$	9,164
Amortization of debt discount and debt issuance costs	4,502		4,097		13,194		12,007
Total interest expense	$	7,557	$	7,152	$	22,392	$	21,171

The following is a summary of interest expense for the Deerfield Notes (in thousands):



	Three Months Ended September 30,				Nine Months Ended September 30,
	2014		2013		2014		2013
Stated coupon interest	$	1,512	$	1,513	$	4,487	$	4,488
Amortization of debt discount and debt issuance costs	3,005		2,555		8,631		7,438
Total interest expense	$	4,517	$	4,068	$	13,118	$	11,926

- 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 505
-SubTopic 10
-Section 50
-Paragraph 3
-URI http://asc.fasb.org/extlink&oid=6928386&loc=d3e21475-112644

Reference 3: 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 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=26873400&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=34725769&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 505
-SubTopic 10
-Section 50
-Paragraph 6
-URI http://asc.fasb.org/extlink&oid=6928386&loc=d3e21506-112644

Reference 8: 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 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

Common Stock And Warrants (Tables)

9 Months Ended

Sep. 30, 2014

Warrants and Rights Note Disclosure [Abstract]

Schedule Of Warrants To Purchase Common Stock Outstanding And Exercisable

At September 30, 2014, the following warrants to purchase common stock were outstanding and exercisable:



Date Issued	Exercise Price per Share		Expiration Date	Number of Shares
January 22, 2014	$	9.70	January 22, 2016	1,000,000

- Definition

Tabular disclosure of warrants or rights issued. Warrants and rights outstanding are derivative securities that give the holder the right to purchase securities (usually equity) from the issuer at a specific price within a certain time frame. Warrants are often included in a new debt issue to entice investors by a higher return potential. The main difference between warrants and call options is that warrants are issued and guaranteed by the company, whereas options are exchange instruments and are not issued by the company. Also, the lifetime of a warrant is often measured in years, while the lifetime of a typical option is measured in months. Disclose the title of issue of securities called for by warrants and rights outstanding, the aggregate amount of securities called for by warrants and rights outstanding, the date from which the warrants or rights are exercisable, and the price at which the warrant or right is exercisable.

+ References + Details

Fair Value Measurements Fair Value Measurements (Tables)

9 Months Ended

Sep. 30, 2014

Fair Value Disclosures [Abstract]

Schedule Of Fair Value Of Financial Assets Measured On A Recurring Basis

The amounts presented exclude cash, but include investments classified as cash equivalents (in thousands):



	September 30, 2014
	Level 1		Level 2		Level 3		Total
Financial assets:
Money market funds	$	41,853	$	—	$	—	$	41,853
Commercial paper	—		72,346		—		72,346
Corporate bonds	—		155,098		—		155,098
U.S. Treasury and government sponsored enterprises	—		12,210		—		12,210
Municipal bonds	—		8,236		—		8,236
Total financial assets	$	41,853	$	247,890	$	—	$	289,743
Financial liabilities:
Warrants	$	—	$	—	$	846	$	846
Total financial liabilities	$	—	$	—	$	846	$	846



	December 31, 2013
	Level 1		Level 2		Total
Money market funds	$	24,813	$	—	$	24,813
Commercial paper	—		94,682		94,682
Corporate bonds	—		240,072		240,072
U.S. Treasury and government sponsored enterprises	—		44,386		44,386
Municipal bonds	—		6,013		6,013
Total financial assets	$	24,813	$	385,153	$	409,966

Schedule Of Estimated Fair Value Of Outstanding Debt

The estimated fair values of our financial instruments that are carried at amortized cost for which it is practicable to determine a fair value were as follows (in thousands):



	September 30, 2014				December 31, 2013
	Carrying Amount		Fair Value		Carrying Amount		Fair Value
2019 Notes	$	177,962	$	159,850	$	165,296	$	339,883
Silicon Valley Bank term loan	$	80,000	$	79,958	$	80,000	$	79,946
Silicon Valley Bank line of credit	$	757	$	757	$	2,090	$	2,090

Schedule of Assumptions Used

The fair value of the 2014 Deerfield Warrants were estimated using the following assumptions, which, except for risk-free interest rate, are Level 3 inputs (dollars in thousands):



	September 30, 2014			January 22, 2014 (issuance date)
Fair value of warrants	$	846		$	2,762
Risk-free interest rate	0.99		%	0.95		%
Dividend yield	—		%	—		%
Volatility	95		%	57		%
Average expected life	3.3 years			3.2 years

Stock-Based Compensation (Tables)

9 Months Ended

Sep. 30, 2014

Share-based Compensation [Abstract]

Schedule Of Allocated Employee Stock-Based Compensation Expenses

We recorded and allocated employee stock-based compensation expenses for our equity incentive plans and our 2000 Employee Stock Purchase Plan (“ESPP”) as follows (in thousands):



	Three Months Ended September 30,					Nine Months Ended September 30,
	2014			2013		2014			2013
Research and development expense	$	112		$	1,415	$	3,148		$	4,326
Selling, general and administrative expense	624			1,478		5,328			4,115
Restructuring-related stock-based compensation (recovery) expense	(22		)	—		(22		)	49
Total employee stock-based compensation expense	$	714		$	2,893	$	8,454		$	8,490

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

The fair value of employee stock option awards and ESPP purchases was estimated using the following assumptions and weighted average fair values:



	Stock Options
	Three Months Ended September 30,						Nine Months Ended September 30,
	2014			2013			2014			2013
Weighted average grant-date fair value	$	1.19		$	2.99		$	1.47		$	2.92
Risk-free interest rate	1.83		%	1.57		%	1.81		%	1.47		%
Dividend yield	—		%	—		%	—		%	—		%
Volatility	86		%	60		%	85		%	60		%
Expected life	5.5 years			5.6 years			5.5 years			5.6 years



	Employee Stock Purchase Plan
	Three Months Ended September 30,						Nine Months Ended September 30,
	2014			2013			2014			2013
Weighted average grant-date fair value	$	1.21		$	1.74		$	1.35		$	1.66
Risk-free interest rate	0.05		%	0.08		%	0.06		%	0.12		%
Dividend yield	—		%	—		%	—		%	—		%
Volatility	68		%	67		%	66		%	67		%
Expected life	6 months			6 months			6 months			6 months

Summary Of All Stock Option Activity

A summary of all stock option activity for the nine months ended September 30, 2014 is presented below (dollars in thousands, except per share amounts):



	Shares		Weighted Average Exercise Price		Weighted Average Remaining Contractual Term	Aggregate Intrinsic Value
Options outstanding at December 31, 2013	23,983,275		$	6.48
Granted	9,653,615		$	2.13
Exercised	(19,090	)	$	6.28
Forfeited	(882,864	)	$	5.53
Expired	(669,778	)	$	7.31
Options outstanding at September 30, 2014	32,065,158		$	5.18	4.81 years	$	—
Exercisable September 30, 2014	15,478,788		$	6.93	3.21 years	$	—

Summary Of All RSU Activity

A summary of all restricted stock unit (“RSU”) activity for the nine months ended September 30, 2014 is presented below (dollars in thousands, except per share amounts):



	Shares		Weighted Average Grant Date Fair Value		Weighted Average Remaining Contractual Term	Aggregate Intrinsic Value
Awards outstanding at December 31, 2013	1,810,521		$	5.56
Awarded	64,637		$	5.11
Released	(114,704	)	$	6.68
Forfeited	(98,073	)	$	5.44
Awards outstanding at September 30, 2014	1,662,381		$	5.48	2.72 years	$	2,593

Net Loss Per Share (Tables)

9 Months Ended

Sep. 30, 2014

Earnings Per Share [Abstract]

Schedule Of Reconciliation Of Basic And Diluted Net Income (Loss) Per Share

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



	Three Months Ended September 30,						Nine Months Ended September 30,
	2014			2013			2014			2013
Numerator:
Net loss	$	(62,560	)	$	(67,124	)	$	(210,589	)	$	(174,014	)
Denominator:
Shares used in computing basic and diluted net loss per share	195,126			184,149			193,855			183,957
Net loss per share, basic and diluted	$	(0.32	)	$	(0.36	)	$	(1.09	)	$	(0.95	)

Schedule Of Potential Shares Of Common Stock Not Included In Computation Of Diluted Net Loss Per Share



	September 30
	2014	2013
Convertible debt	75,734	54,123
Outstanding stock options, unvested RSUs and ESPP contributions	34,243	25,694
Warrants	1,000	1,441
Total potentially dilutive shares	110,977	81,258

Concentrations of Credit Risk (Tables)

9 Months Ended

Sep. 30, 2014

Risks and Uncertainties [Abstract]

Schedules of concentration risk

The following table shows the percentage of revenues earned in the United States and the European Union.



	Three Months Ended September 30,				Nine Months Ended September 30,
	2014		2013		2014		2013
Percentage of revenues earned in the United States	108	%	87	%	100	%	96	%
Percentage of revenues earned in the European Union	(8	)%	13	%	—	%	4	%



	Three Months Ended September 30,				Nine Months Ended September 30,
	2014		2013		2014		2013
Collaboration agreement:
Bristol-Myers Squibb	—	%	13	%	—	%	60	%
Product sales:
Diplomat Specialty Pharmacy	108	%	74	%	100	%	36	%

Organization and Summary of Significant Accounting Policies (Details)	9 Months Ended
	Sep. 30, 2014 segment trial	Sep. 30, 2013
Operations [Line Items]
Number of trials in process	45
Number of Phase 3 Trials in Process	3
Operating cycle	371 days	364 days
Number of operating segments \| segment	1
Glaxo Smith Kline [Member]
Operations [Line Items]
Percent of royalty on net sale	3.00%
Minimum [Member]
Operations [Line Items]
Operating cycle	364 days
Maximum [Member]
Operations [Line Items]
Operating cycle	371 days

Restructurings (Narrative) (Details) $ in Thousands		3 Months Ended		9 Months Ended		39 Months Ended
Restructurings (Narrative) (Details) $ in Thousands	Sep. 02, 2014 USD ($) employee	Sep. 30, 2014 USD ($) employee	Sep. 30, 2013 USD ($)	Sep. 30, 2014 USD ($) employee	Sep. 30, 2013 USD ($)	May 31, 2013 restructuring	Dec. 31, 2013 USD ($)
Restructuring Cost and Reserve [Line Items]
Restructuring charge (credit)		$ 3,758	$ 137	$ 4,135	$ 865
2014 Restructuring [Member]
Restructuring Cost and Reserve [Line Items]
Number of positions eliminated, percent	65.00%
Expected number of positions eliminated \| employee	150
Expected number of remaining positions \| employee	80
Restructuring charge (credit)				3,308
Adjustments or non-cash credits				(645)
Restructuring reserve		2,601		2,601
2014 Restructuring [Member] \| One-time Termination Benefits [Member]
Restructuring Cost and Reserve [Line Items]
Expected restructuring cost, percentage in current fiscal year	95.00%
2014 Restructuring [Member] \| One-time Termination Benefits [Member] \| Minimum [Member]
Restructuring Cost and Reserve [Line Items]
Expected restructuring charges	$ 6,000
2014 Restructuring [Member] \| One-time Termination Benefits [Member] \| Maximum [Member]
Restructuring Cost and Reserve [Line Items]
Expected restructuring charges	$ 7,000
2014 Restructuring [Member] \| Employee Severance and Other Benefits [Member]
Restructuring Cost and Reserve [Line Items]
Restructuring charge (credit)				2,591
Adjustments or non-cash credits				22
Restructuring reserve		2,551		2,551
2014 Restructuring [Member] \| Asset Impairment and Other [Member]
Restructuring Cost and Reserve [Line Items]
Restructuring charge (credit)				717
Adjustments or non-cash credits				(667)
Restructuring reserve		50		50
2010 Restructurings [Member]
Restructuring Cost and Reserve [Line Items]
Expected restructuring charges		$ 900		900
Restructuring charge (credit)				827	$ 800
Adjustments or non-cash credits				$ (78)
Number of restructurings implemented \| restructuring						5
Aggregate reduction in headcount \| employee		429		429
Restructuring reserve		$ 9,500		$ 9,500			$ 13,472
2010 Restructurings [Member] \| Other [Member]
Restructuring Cost and Reserve [Line Items]
Restructuring charge (credit)				(113)
Adjustments or non-cash credits				(86)
Restructuring reserve		6		6			12
2010 Restructurings [Member] \| Facility Closing [Member]
Restructuring Cost and Reserve [Line Items]
Restructuring charge (credit)				940
Adjustments or non-cash credits				8
Restructuring reserve		$ 9,494		$ 9,494			$ 13,460

Restructurings (Summary of Components of Restructuring Liability) (Details) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2014	Sep. 30, 2013	Sep. 30, 2014	Sep. 30, 2013
Restructuring Reserve [Roll Forward]
Restructuring charge (credit)	$ 3,758	$ 137	$ 4,135	$ 865
2014 Restructuring [Member]
Restructuring Reserve [Roll Forward]
Restructuring charge (credit)			3,308
Cash payments			(62)
Adjustments or non-cash credits			(645)
Restructuring liability	2,601		2,601
2014 Restructuring [Member] \| Employee Severance and Other Benefits [Member]
Restructuring Reserve [Roll Forward]
Restructuring charge (credit)			2,591
Cash payments			(62)
Adjustments or non-cash credits			22
Restructuring liability	2,551		2,551
2014 Restructuring [Member] \| Asset Impairment and Other [Member]
Restructuring Reserve [Roll Forward]
Restructuring charge (credit)			717
Cash payments			0
Adjustments or non-cash credits			(667)
Restructuring liability	50		50
2010 Restructurings [Member]
Restructuring Reserve [Roll Forward]
Restructuring liability			13,472
Restructuring charge (credit)			827	$ 800
Cash payments			(4,920)
Adjustments or non-cash credits			(78)
Proceeds from sale of assets			199
Restructuring liability	9,500		9,500
2010 Restructurings [Member] \| Facility Charges [Member]
Restructuring Reserve [Roll Forward]
Restructuring liability			13,460
Restructuring charge (credit)			940
Cash payments			(4,914)
Adjustments or non-cash credits			8
Proceeds from sale of assets			0
Restructuring liability	9,494		9,494
2010 Restructurings [Member] \| Other [Member]
Restructuring Reserve [Roll Forward]
Restructuring liability			12
Restructuring charge (credit)			(113)
Cash payments			(6)
Adjustments or non-cash credits			(86)
Proceeds from sale of assets			199
Restructuring liability	$ 6		$ 6

Cash and Investments Cash and Investments (Details)	9 Months Ended
Cash and Investments Cash and Investments (Details)	Sep. 30, 2014 USD ($) account affiliate investment	Sep. 30, 2013 USD ($)	Dec. 31, 2013 USD ($)
Schedule of Available-for-sale Securities [Line Items]
Amortized Cost	$ 293,353,000		$ 415,617,000
Gross Unrealized Gains	213,000		300,000
Gross Unrealized Losses	(81,000)		(55,000)
Fair Value	$ 293,485,000		415,862,000
Debt collateral, number of required investment accounts \| account	1
Debt collateral, number of affiliate banks \| affiliate	1
Amortized Cost	$ 289,611,000		409,721,000
Gross Unrealized Gains	213,000		300,000
Gross Unrealized Losses	(81,000)		(55,000)
Fair Value	289,743,000		409,966,000
Gain (loss) on sale of investments	$ 0	$ 0
Number of investments in an unrealized loss position, less than 1 year \| investment	35
Unrealized loss position, less than 1 year	$ 64,600,000
Number of investments in an unrealized loss position, greater than 1 year \| investment	0
Unrealized loss position, greater than 1 year	$ 0
Mature within One Year	267,951,000
After One Year through Two Years	21,792,000
Fair Value	289,743,000		409,966,000
Money market funds [Member]
Schedule of Available-for-sale Securities [Line Items]
Amortized Cost	41,853,000		24,813,000
Gross Unrealized Gains	0		0
Gross Unrealized Losses	0		0
Fair Value	41,853,000		24,813,000
Mature within One Year	41,853,000
After One Year through Two Years	0
Fair Value	41,853,000		24,813,000
Commercial paper [Member]
Schedule of Available-for-sale Securities [Line Items]
Amortized Cost	72,346,000		94,682,000
Gross Unrealized Gains	0		0
Gross Unrealized Losses	0		0
Fair Value	72,346,000		94,682,000
Mature within One Year	72,346,000
After One Year through Two Years	0
Fair Value	72,346,000		94,682,000
Corporate bonds [Member]
Schedule of Available-for-sale Securities [Line Items]
Amortized Cost	155,078,000		239,937,000
Gross Unrealized Gains	101,000		190,000
Gross Unrealized Losses	(81,000)		(55,000)
Fair Value	155,098,000		240,072,000
Mature within One Year	133,306,000
After One Year through Two Years	21,792,000
Fair Value	155,098,000		240,072,000
U.S. Treasury and government sponsored enterprises [Member]
Schedule of Available-for-sale Securities [Line Items]
Amortized Cost	12,105,000		44,284,000
Gross Unrealized Gains	105,000		102,000
Gross Unrealized Losses	0		0
Fair Value	12,210,000		44,386,000
Mature within One Year	12,210,000
After One Year through Two Years	0
Fair Value	12,210,000		44,386,000
Municipal bonds [Member]
Schedule of Available-for-sale Securities [Line Items]
Amortized Cost	8,229,000		6,005,000
Gross Unrealized Gains	7,000		8,000
Gross Unrealized Losses	0
Fair Value	8,236,000		6,013,000
Mature within One Year	8,236,000
After One Year through Two Years	0
Fair Value	8,236,000		6,013,000
Silicon Valley Bank Loan And Security Agreement [Member]
Schedule of Available-for-sale Securities [Line Items]
Collateral balance	82,400,000		83,700,000
Cash and cash equivalents [Member]
Schedule of Available-for-sale Securities [Line Items]
Amortized Cost	100,065,000		103,978,000
Gross Unrealized Gains	0		0
Gross Unrealized Losses	0		0
Fair Value	100,065,000		103,978,000
Short-term investments [Member]
Schedule of Available-for-sale Securities [Line Items]
Amortized Cost	91,898,000		138,403,000
Gross Unrealized Gains	88,000		94,000
Gross Unrealized Losses	(49,000)		(22,000)
Fair Value	91,937,000		138,475,000
Short-term restricted cash and investments [Member]
Schedule of Available-for-sale Securities [Line Items]
Amortized Cost	12,105,000		12,173,000
Gross Unrealized Gains	105,000		40,000
Gross Unrealized Losses	0		0
Fair Value	12,210,000		12,213,000
Long-term investments [Member]
Schedule of Available-for-sale Securities [Line Items]
Amortized Cost	84,601,000		144,226,000
Gross Unrealized Gains	20,000		106,000
Gross Unrealized Losses	(32,000)		(33,000)
Fair Value	84,589,000		144,299,000
Long-term restricted cash and investments [Member]
Schedule of Available-for-sale Securities [Line Items]
Amortized Cost	4,684,000		16,837,000
Gross Unrealized Gains	0		60,000
Gross Unrealized Losses	0		0
Fair Value	$ 4,684,000		$ 16,897,000

Inventory (Details) - USD ($)
$ in Thousands

Sep. 30, 2014

Dec. 31, 2013

Inventory Disclosure [Abstract]

Raw materials

$ 787

$ 529

Work in process

2,501

2,280

Finished goods

588

Total

$ 3,876

$ 2,890

^[1]

[1]	The condensed consolidated balance sheet as of December 31, 2013 has been derived from the audited financial statements as of that date.

Debt (Schedule Of Debt) (Details) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
Debt (Schedule Of Debt) (Details) - USD ($) $ in Thousands	Sep. 30, 2014	Sep. 30, 2013	Sep. 30, 2014	Sep. 30, 2013	Dec. 31, 2013
Debt Instrument [Line Items]
Total debt	$ 355,215		$ 355,215		$ 347,237
Less: current portion	(97,253)		(97,253)		(11,762)
Long-term debt	257,962		257,962		335,475
Senior Subordinated Notes [Member] \| 4.25% Convertible Senior Subordinated Notes due August 15, 2019 [Member]
Debt Instrument [Line Items]
Stated coupon interest	3,055	$ 3,055	9,198	$ 9,164
Convertible Debt	177,962		177,962		165,296
Amortization of debt discount and debt issuance costs	4,502	4,097	13,194	12,007
Interest Expense, Debt	7,557	$ 7,152	22,392	$ 21,171
Secured Debt [Member] \| Deerfield Notes [Member]
Debt Instrument [Line Items]
Convertible Debt	96,496		96,496		99,851
Term Loan [Member] \| Silicon Valley Bank term loan and Line of Credit [Member]
Debt Instrument [Line Items]
Silicon Valley Bank term loan	80,000		80,000		80,000
Line of Credit [Member] \| Silicon Valley Bank term loan and Line of Credit [Member]
Debt Instrument [Line Items]
Silicon Valley Bank Line of Credit	$ 757		$ 757		$ 2,090

Debt (Convertible Notes) (Details) - USD ($)	3 Months Ended		9 Months Ended
Debt (Convertible Notes) (Details) - USD ($)	Sep. 30, 2014	Sep. 30, 2013	Sep. 30, 2014	Sep. 30, 2013	Dec. 31, 2013	Aug. 14, 2012	Jun. 30, 2010
Senior Subordinated Notes [Member] \| 4.25% Convertible Senior Subordinated Notes due August 15, 2019 [Member]
Debt Instrument [Line Items]
Net carrying amount of the liability component	$ 177,962,000		$ 177,962,000		$ 165,296,000
Unamortized discount of the liability component	109,538,000		109,538,000		122,204,000
Face amount	287,500,000		287,500,000		287,500,000	$ 287,500,000
Stated coupon interest	3,055,000	$ 3,055,000	9,198,000	$ 9,164,000
Amortization of debt discount and debt issuance costs	4,502,000	4,097,000	13,194,000	12,007,000
Total interest expense	7,557,000	7,152,000	22,392,000	21,171,000
Secured Convertible Notes Due June 2015 [Member] \| Deerfield Financing [Member]
Debt Instrument [Line Items]
Net carrying amount of the liability component	104,000,000		104,000,000		$ 114,000,000
Face amount							$ 124,000,000.0
Stated coupon interest	1,512,000	1,513,000	4,487,000	4,488,000
Amortization of debt discount and debt issuance costs	3,005,000	2,555,000	8,631,000	7,438,000
Total interest expense	$ 4,517,000	$ 4,068,000	$ 13,118,000	$ 11,926,000

Debt (Narrative) (Details) - USD ($)	Jan. 22, 2014	Jan. 22, 2014	Sep. 30, 2014	Dec. 31, 2013	Aug. 14, 2012	Jun. 30, 2010
Issued On January 22, 2014 [Member]
Debt Instrument [Line Items]
Warrant period	2 years	2 years
Warrants outstanding	1,000,000	1,000,000	1,000,000
Warrant exercise price (in dollars per warrant)	$ 9.70	$ 9.70	$ 9.70
Senior Subordinated Notes [Member] \| 4.25% Convertible Senior Subordinated Notes due August 15, 2019 [Member]
Debt Instrument [Line Items]
Debt, interest rate					4.25%
Debt, principal amount			$ 287,500,000	$ 287,500,000	$ 287,500,000
Balance of unamortized closing fees and expenses			3,400,000	4,000,000
Convertible debt			177,962,000	165,296,000
Secured Convertible Notes Due June 2015 [Member] \| Deerfield Financing [Member]
Debt Instrument [Line Items]
Debt, principal amount						$ 124,000,000.0
Balance of unamortized closing fees and expenses			2,100,000	1,400,000
Convertible debt			$ 104,000,000	$ 114,000,000
Principal eligible for extension option	$ 100,000,000	$ 100,000,000
Debt instrument, interest rate, stated percentage after extension option election	15.00%	15.00%
Debt instrument, discount	$ 2,800,000	$ 2,800,000
Secured Convertible Notes Due June 2015 [Member] \| Deerfield Financing [Member] \| Coupon Interest [Member]
Debt Instrument [Line Items]
Debt instrument, interest rate, stated percentage after extension option election	7.50%	7.50%
Secured Convertible Notes Due June 2015 [Member] \| Deerfield Financing [Member] \| Payment-in-Kind Interest [Member]
Debt Instrument [Line Items]
Debt instrument, interest rate, stated percentage after extension option election	7.50%	7.50%

Common Stock And Warrants (Narrative) (Details) - USD ($) $ / shares in Units, $ in Thousands			1 Months Ended	3 Months Ended	9 Months Ended
	Jan. 22, 2014	Jan. 22, 2014	Jan. 31, 2014	Sep. 30, 2014	Sep. 30, 2014	Sep. 30, 2013
Class of Warrant or Right [Line Items]
Public offering of common stock			10,000,000
Share price (dollars per share)			$ 8
Net proceeds from public offering			$ 75,600		$ 75,646	$ 0
Issued On January 22, 2014 [Member]
Class of Warrant or Right [Line Items]
Warrants outstanding	1,000,000	1,000,000		1,000,000	1,000,000
Warrant exercise price (in dollars per warrant)	$ 9.70	$ 9.70		$ 9.70	$ 9.70
Warrant period	2 years	2 years
Warrant repricing terms on exercise of extension option	120.00%	120.00%
Fair value of warrants	$ 2,800	$ 2,800		$ 800	$ 800
Unrealized gain on warrants				$ 100	$ 1,900

Common Stock And Warrants (Schedule Of Warrants To Purchase Common Stock Outstanding And Exercisable) (Details) - Issued On January 22, 2014 [Member] - $ / shares	9 Months Ended
	Sep. 30, 2014	Jan. 22, 2014
Class of Warrant or Right [Line Items]
Exercise Price per Share	$ 9.70	$ 9.70
Expiration Date	1/22/2016
Number of Shares	1,000,000	1,000,000

Fair Value Measurements (Schedule Of Fair Value Of Financial Assets Measured On A Recurring Basis) (Details) - USD ($) $ in Thousands	Sep. 30, 2014	Dec. 31, 2013
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Total fair value of financial assets	$ 289,743	$ 409,966
Warrants	846
Total financial liabilities	846
Level 1 [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Total fair value of financial assets	41,853	24,813
Warrants	0
Total financial liabilities	0
Level 2 [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Total fair value of financial assets	247,890	385,153
Warrants	0
Total financial liabilities	0
Level 3 [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Total fair value of financial assets	0
Warrants	846
Total financial liabilities	846
Money market funds [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Total fair value of financial assets	41,853	24,813
Money market funds [Member] \| Level 1 [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Total fair value of financial assets	41,853	24,813
Money market funds [Member] \| Level 2 [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Total fair value of financial assets	0	0
Money market funds [Member] \| Level 3 [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Total fair value of financial assets	0
Commercial paper [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Total fair value of financial assets	72,346	94,682
Commercial paper [Member] \| Level 1 [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Total fair value of financial assets	0	0
Commercial paper [Member] \| Level 2 [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Total fair value of financial assets	72,346	94,682
Commercial paper [Member] \| Level 3 [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Total fair value of financial assets	0
Corporate bonds [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Total fair value of financial assets	155,098	240,072
Corporate bonds [Member] \| Level 1 [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Total fair value of financial assets	0	0
Corporate bonds [Member] \| Level 2 [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Total fair value of financial assets	155,098	240,072
Corporate bonds [Member] \| Level 3 [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Total fair value of financial assets	0
U.S. Treasury and government sponsored enterprises [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Total fair value of financial assets	12,210	44,386
U.S. Treasury and government sponsored enterprises [Member] \| Level 1 [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Total fair value of financial assets	0	0
U.S. Treasury and government sponsored enterprises [Member] \| Level 2 [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Total fair value of financial assets	12,210	44,386
U.S. Treasury and government sponsored enterprises [Member] \| Level 3 [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Total fair value of financial assets	0
Municipal bonds [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Total fair value of financial assets	8,236	6,013
Municipal bonds [Member] \| Level 1 [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Total fair value of financial assets	0	0
Municipal bonds [Member] \| Level 2 [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Total fair value of financial assets	8,236	$ 6,013
Municipal bonds [Member] \| Level 3 [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Total fair value of financial assets	$ 0

Fair Value Measurements (Schedule of Estimated Fair Value of Outstanding Debt) (Details) - USD ($) $ in Thousands	Sep. 30, 2014	Dec. 31, 2013
Carrying Amount [Member] \| Senior Subordinated Notes [Member] \| 4.25% Convertible Senior Subordinated Notes due August 15, 2019 [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Fair values of financial instruments	$ 177,962	$ 165,296
Carrying Amount [Member] \| Term Loan [Member] \| Silicon Valley Bank term loan and Line of Credit [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Fair values of financial instruments	80,000	80,000
Carrying Amount [Member] \| Line of Credit [Member] \| Silicon Valley Bank term loan and Line of Credit [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Fair values of financial instruments	757	2,090
Fair Value [Member] \| Senior Subordinated Notes [Member] \| 4.25% Convertible Senior Subordinated Notes due August 15, 2019 [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Fair values of financial instruments	159,850	339,883
Fair Value [Member] \| Term Loan [Member] \| Silicon Valley Bank term loan and Line of Credit [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Fair values of financial instruments	79,958	79,946
Fair Value [Member] \| Line of Credit [Member] \| Silicon Valley Bank term loan and Line of Credit [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Fair values of financial instruments	$ 757	$ 2,090

Fair Value Measurements (Schedule of Assumptions Used) (Details) - Issued On January 22, 2014 [Member] - USD ($) $ in Thousands			9 Months Ended
	Jan. 22, 2014	Jan. 22, 2014	Sep. 30, 2014
Fair Value Inputs, Liabilities, Quantitative Information [Line Items]
Warrant period	2 years	2 years
Warrant liability [Member]
Fair Value Inputs, Liabilities, Quantitative Information [Line Items]
Fair value of warrants	$ 2,762	$ 2,762	$ 846
Risk-free interest rate		0.95%	0.99%
Dividend yield		0.00%	0.00%
Volatility		57.00%	95.00%
Average expected life		3 years 2 months 12 days	3 years 3 months 18 days

Stock-Based Compensation (Schedule of Allocated Employee Stock-Based Compensation Expenses) (Details) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2014	Sep. 30, 2013	Sep. 30, 2014	Sep. 30, 2013
Employee Service Share-based Compensation, Allocation of Recognized Period Costs [Line Items]
Total employee stock-based compensation expense	$ 714	$ 2,893	$ 8,454	$ 8,490
Research and development expense [Member]
Employee Service Share-based Compensation, Allocation of Recognized Period Costs [Line Items]
Total employee stock-based compensation expense	112	1,415	3,148	4,326
Selling, general and administrative expense [Member]
Employee Service Share-based Compensation, Allocation of Recognized Period Costs [Line Items]
Total employee stock-based compensation expense	624	1,478	5,328	4,115
Restructuring-related stock-based compensation expense [Member]
Employee Service Share-based Compensation, Allocation of Recognized Period Costs [Line Items]
Total employee stock-based compensation expense	$ (22)	$ 0	$ (22)	$ 49

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, 2014	Sep. 30, 2013	Sep. 30, 2014	Sep. 30, 2013
Employee Stock Option [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Weighted average grant date fair value	$ 1.19	$ 2.99	$ 1.47	$ 2.92
Risk-free interest rate	1.83%	1.57%	1.81%	1.47%
Dividend yield	0.00%	0.00%	0.00%	0.00%
Volatility	86.00%	60.00%	85.00%	60.00%
Expected life	5 years 6 months	5 years 7 months 6 days	5 years 6 months	5 years 7 months 6 days
Employee Stock Purchase Plan [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Weighted average grant date fair value	$ 1.21	$ 1.74	$ 1.35	$ 1.66
Risk-free interest rate	0.05%	0.08%	0.06%	0.12%
Dividend yield	0.00%	0.00%	0.00%	0.00%
Volatility	68.00%	67.00%	66.00%	67.00%
Expected life	6 months	6 months	6 months	6 months

Stock-Based Compensation (Narrative) (Details) - USD ($) $ in Millions	3 Months Ended	9 Months Ended
	Sep. 30, 2014	Sep. 30, 2014	Dec. 31, 2013
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Options outstanding, in shares	32,065,158	32,065,158	23,983,275
Options cancelled, shares		882,864
Performance Stock Options [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Options outstanding, in shares	11,359,106	11,359,106
Grant date fair value	$ 19.0	$ 19.0
Options cancelled, value	$ 2.1
Options cancelled, shares	692,896
Performance Stock Options COMET-2 [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Grant date fair value	$ 1.1	1.1
Employee Stock Option [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Unrecognized compensation expense	28.3	$ 28.3
Unrecognized compensation expense, weighted-average period for recognition (in years)		2 years 8 months 12 days
Restricted Stock Units (RSUs) [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Unrecognized compensation expense	$ 2.0	$ 2.0
Unrecognized compensation expense, weighted-average period for recognition (in years)		2 years 8 months 19 days

Stock-Based Compensation (Summary of All Stock Option Activity) (Details) - USD ($) $ / shares in Units, $ in Thousands	9 Months Ended
	Sep. 30, 2014
Shares [Roll Forward]
Options outstanding at beginning of period, Shares	23,983,275
Granted, Shares	9,653,615
Exercised, Shares	(19,090)
Forfeited, Shares	(882,864)
Expired, Shares	(669,778)
Options outstanding at end of period, Shares	32,065,158
Exercisable at end of period, Shares	15,478,788
Weighted Average Exercise Price [Roll Forward]
Options outstanding at beginning of period, Weighted Average Exercise Price	$ 6.48
Granted, Weighted Average Exercise Price	2.13
Exercised, Weighted Average Exercise Price	6.28
Forfeited, Weighted Average Exercise Price	5.53
Expired, Weighted Average Exercise Price	7.31
Options outstanding at end of period, Weighted Average Exercise Price	5.18
Exercisable at end of period, Weighted Average Exercise Price	$ 6.93
Options outstanding at end of period, Weighted Average Remaining Contractual Term	4 years 9 months 21 days
Exercisable at end of period, Weighted Average Remaining Contractual Term	3 years 2 months 15 days
Options outstanding at end of period, Aggregate Intrinsic Value, in dollars	$ 0
Exercisable at end of period, Aggregate Intrinsic Value, in dollars	$ 0

Stock-Based Compensation (Summary of All RSU Activity) (Details) - Restricted Stock Units (RSUs) [Member] $ / shares in Units, $ in Thousands	9 Months Ended
	Sep. 30, 2014 USD ($) $ / shares shares
Shares [Roll Forward]
RSUs outstanding at beginning of period, Shares \| shares	1,810,521
Awarded, Shares \| shares	64,637
Released, Shares \| shares	(114,704)
Forfeited, Shares \| shares	(98,073)
RSUs outstanding at end of period, Shares \| shares	1,662,381
Weighted Average Grant DateFair Value [Roll Forward]
RSUs outstanding at beginning of period, Weighted Average Grant Date Fair Value \| $ / shares	$ 5.56
Awarded, Weighted Average Grant Date Fair Value \| $ / shares	5.11
Released, Weighted Average Grant Date Fair Value \| $ / shares	6.68
Forfeited, Weighted Average Grant Date Fair Value \| $ / shares	5.44
RSUs outstanding at end of period, Weighted Average Grant Date Fair Value \| $ / shares	$ 5.48
ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsOutstandingWeightedAverageRemainingContractualTerms	2 years 8 months 19 days
RSUs outstanding at end of period, Aggregate Intrinsic Value, in dollars \| $	$ 2,593

Net Loss Per Share (Details) - USD ($) $ / shares in Units, shares in Thousands, $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2014	Sep. 30, 2013	Sep. 30, 2014	Sep. 30, 2013
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Net loss, in dollars	$ (62,560)	$ (67,124)	$ (210,589)	$ (174,014)
Shares used in computing basic and diluted net loss per share	195,126	184,149	193,855	183,957
Net loss per share, basic and diluted, in dollars per share	$ (0.32)	$ (0.36)	$ (1.09)	$ (0.95)
Potentially dilutive shares			110,977	81,258
Convertible debt [Member]
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Potentially dilutive shares			75,734	54,123
Outstanding stock options, unvested RSUs and ESPP contributions [Member]
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Potentially dilutive shares			34,243	25,694
Warrants [Member]
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Potentially dilutive shares			1,000	1,441

- Definition

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

+ References + Details

Concentrations of Credit Risk (Details) - USD ($) $ in Millions	3 Months Ended		9 Months Ended
	Sep. 30, 2014	Sep. 30, 2013	Sep. 30, 2014	Sep. 30, 2013
European Distribution Partner [Member]
Concentration Risk [Line Items]
Reduction to net product revenues	$ 1.8
Customer Concentration Risk [Member] \| Accounts Receivable [Member] \| Diplomat Specialty Pharmacy [Member]
Concentration Risk [Line Items]
Concentration risk, percentage			74.00%
Customer Concentration Risk [Member] \| Accounts Receivable [Member] \| European Distribution Partner [Member]
Concentration Risk [Line Items]
Concentration risk, percentage			15.00%
Customer Concentration Risk [Member] \| Revenue, Rights Granted [Member] \| Bristol-Myers Squibb [Member]
Concentration Risk [Line Items]
Concentration risk, percentage	0.00%	13.00%	0.00%	60.00%
Customer Concentration Risk [Member] \| Sales Revenue, Goods, Net [Member] \| Diplomat Specialty Pharmacy [Member]
Concentration Risk [Line Items]
Concentration risk, percentage	108.00%	74.00%	100.00%	36.00%
United States [Member] \| Geographic Concentration Risk [Member] \| Sales [Member]
Concentration Risk [Line Items]
Concentration risk, percentage	108.00%	87.00%	100.00%	96.00%
European Union [Member] \| Geographic Concentration Risk [Member] \| Sales [Member]
Concentration Risk [Line Items]
Concentration risk, percentage	(8.00%)	13.00%	0.00%	4.00%

Disposition of Artemis Pharmaceuticals (Details) - USD ($) $ in Thousands	1 Months Ended			9 Months Ended
	Sep. 30, 2014	Sep. 30, 2011	Nov. 30, 2007	Sep. 30, 2014	Sep. 30, 2013
Income Statement, Balance Sheet and Additional Disclosures by Disposal Groups, Including Discontinued Operations [Line Items]
Proceeds from sale of business				$ 838	$ 0
Artemis Pharmaceuticals GmbH [Member]
Income Statement, Balance Sheet and Additional Disclosures by Disposal Groups, Including Discontinued Operations [Line Items]
Ownership percentage sold		19.90%	80.10%
Proceeds from sale of business	$ 800
Gain on disposal	$ 800