As Filed with the Securities and Exchange Commission on March 10, 2004
                                                           Registration No. 333-
================================================================================
                       SECURITIES AND EXCHANGE COMMISSION
                             Washington, D.C.  20549
                                    FORM S-8
                             REGISTRATION STATEMENT
                                      UNDER
                           THE SECURITIES ACT OF 1933

                                 EXELIXIS, INC.
             (Exact name of registrant as specified in its charter)

           Delaware                                 04-3257395
    (State of Incorporation)          (I.R.S. Employer Identification Number)

                                 170 Harbor Way
                                  P.O. Box 511
                          South San Francisco, CA 94083
                                 (650) 837-7000
                    (Address of principal executive offices)
                    ----------------------------------------

                           2000 EQUITY INCENTIVE PLAN
                        2000 EMPLOYEE STOCK PURCHASE PLAN
                            (Full title of the plans)

                                   Frank Karbe
                             Chief Financial Officer
                                 Exelixis, Inc.
                                 170 Harbor Way
                                  P.O. Box 511
                          South San Francisco, CA 94083
                                 (650) 837-7000
  (Name, address, including zip code, and telephone number, including area code,
                              of agent for service)

                                   Copies to:

                              Robert L. Jones, Esq.
                               Cooley Godward LLP
                              Five Palo Alto Square
                               3000 El Camino Real
                           Palo Alto, California 94306



                                            CALCULATION OF REGISTRATION FEE
=======================================================================================================================
                                                                                  Proposed Maximum
     Title of Securities           Amount to be      Proposed Maximum Offering   Aggregate Offering       Amount of
      to be Registered             Registered(1)        Price Per Share (2)           Price (2)        Registration Fee
- ------------------------------  -----------------  ---------------------------  --------------------  -----------------
                                                                                          
- ------------------------------  -----------------  ---------------------------  --------------------  -----------------
Stock Options and Common Stock   1,599,429 shares             $8.76                  $14,010,998           $1,775.19
(par value $.001)
=======================================================================================================================


(1)  Pursuant  to  Rule 416(a) under the Securities Act of 1933, as amended (the
     "Securities  Act"),  this  Registration  Statement  shall  also  cover  any
     additional  shares  of  the  registrant's common stock that become issuable
     under  the 2000 Equity Incentive Plan and 2000 Employee Stock Purchase Plan
     by reason of any stock dividend, stock split, recapitalization or any other
     similar  transaction.

(2)  Estimated  solely  for  the  purpose  of  calculating  the  amount  of  the
     registration  fee  pursuant  to Rule 457(c) and (h)(1) under the Securities
     Act.  The  offering  price  per  share and aggregate offering price for the
     unissued  stock  options  and  shares  of  common  stock are based upon the
     average  of  the  high  and  low prices of the Registrant's common stock as
     reported  on  the  Nasdaq  National  Market  System  on  March 9, 2004. The
     following  chart  illustrates  the  calculation  of  the  registration fee:




                                                                                         Proposed Maximum       Proposed Maximum
                                                                     Amount to be          Offering Price       Aggregate Offering
Title of Shares to be Registered                                      Registered             Per Share               Price
- --------------------------------                                  -------------------    -------------------   --------------------
                                                                                                  
Shares issuable pursuant to the 2000 Equity Incentive Plan                1,000,000             $8.76               $8,760,000

Shares issuable pursuant to the Employee Stock Purchase Plan                599,429             $8.76               $5,250,998

Proposed Maximum Aggregate Offering Price                                                                          $14,010,998



     Approximate  date  of commencement of proposed sale to the public:  as soon
as  practicable  after  this  Registration  Statement  becomes  effective.

EXPLANATORY NOTE This Registration Statement on Form S-8 is being filed for the purpose of registering an additional: (i) 1,000,000 shares of the Registrant's common stock to be issued pursuant to the Registrant's 2000 Equity Incentive Plan and (ii) 599,429 shares of the Registrant's common stock to be issued pursuant to the Registrant's 2000 Employee Stock Purchase Plan. INCORPORATION OF CERTAIN DOCUMENTS BY REFERENCE The contents of the Registration Statements on Form S-8 (relating to the 2000 Equity Incentive Plan and 2000 Employee Stock Purchase Plan) File Nos. 333-35862, 333-57026, 333-82722 and 333-102770 previously filed with the SEC on April 28, 2000, March 14, 2001, February 14, 2002 and January 28, 2003, respectively, are incorporated by reference herein. Item 8. Exhibits Exhibit Number Description 4.1 Specimen Common Stock Certificate. (1) 4.2 Fourth Amended and Restated Registration Rights Agreement, dated February 26, 1999 among Exelixis, Inc. and Certain Stockholders of Exelixis,Inc. (1) 4.3 Warrant, dated August 17, 1998, to purchase 125,796 post-split shares of Exelixis, Inc. Series A preferred stock in favor of Comdisco, Inc. (1) 4.4 Warrant, dated August 17, 1998, to purchase 15,365 post-split shares of Exelixis, Inc. Series A preferred stock in favor of Greg Stento. (1) 4.5 Warrant, dated January 24, 1996, to purchase 267,857 post-split shares of Exelixis, Inc. Series B convertible stock in favor of MMC/GATX Partnership No. 1. (1) 4.6 Warrant, dated September 25, 1997, to purchase 63,750 post-split shares of Exelixis, Inc. common stock in favor of MMC/GATX Partnership No. 1. (1) 4.7 Warrant, dated November 15, 1999, to purchase 9,000 post-split shares of Exelixis, Inc. common stock in favor Bristow Investments, L.P. (1) 4.8 Warrant, dated November 15, 1999, to purchase 101,250 post-split shares of Exelixis, Inc. common stock in favor of Slough Estates USA, Inc. (1) 4.9 Warrant, dated November 15, 1999, to purchase 2,250 post-split shares of Exelixis, Inc. common stock in favor of Laurence and Magdalena Shushan Trust. (1) 4.10 Warrant, dated April 1, 2000, to purchase 70,875 shares of Exelixis, Inc. common stock in favor of Slough Estates USA, Inc. (2) 4.11 Warrant, dated April 1, 2000, to purchase 6,300 shares of Exelixis, Inc. common stock in favor of Bristow Investments, L.P. (2) 4.12 Warrant, dated April 1, 2000, to purchase 1,575 shares of Exelixis, Inc. common stock in favor of Laurance and Madgalena Shusan Family Trust. (2) 4.13 Form of Convertible Promissory Note, dated May 22, 2001 by and between Exelixis, Inc. and Protein Design Labs, Inc. (3) 4.14 Form of Note Purchase Agreement, dated May 22, 2001 by and between Exelixis, Inc. and Protein Design Labs, Inc. (3) 5.1 Opinion of Cooley Godward LLP. 23.1 Consent of Ernst & Young LLP, Independent Auditors. 23.2 Consent of Cooley Godward LLP (contained in Exhibit 5.1 to this Registration Statement). 24.1 Power of Attorney (contained on the signature pages to this Registration Statement). 99.1 2000 Equity Incentive Plan. (1) 99.2 2000 Employee Stock Purchase Plan. (1) ________________________ (1) Filed as an Exhibit to Exelixis, Inc.'s Registration Statement on Form S-1, as amended (File No. 333-30978), as filed with the Securities and Exchange Commission on February 7, 2000, as amended, and incorporated herein by reference. (2) Filed as an Exhibit to Exelixis, Inc.'s Quarterly Report on Form 10-Q for the quarter ended March 31, 2000, filed with the Securities and Exchange Commission on May 15, 2000 and incorporated herein by reference. (3) Filed as an Exhibit to Exelixis, Inc.'s Quarterly Report on Form 10-Q for the quarter ended June 30, 2001, as filed with the Securities and Exchange Commission on August 14, 2001 and incorporated herein by reference.

SIGNATURES Pursuant to the requirements of the Securities Act of 1933, as amended, the Registrant certifies that it has reasonable grounds to believe that it meets all of the requirements for filing on Form S-8 and has duly caused this Registration Statement to be signed on its behalf by the undersigned, thereunto duly authorized, in the City of South San Francisco, State of California, on March 10, 2004. EXELIXIS, INC. By: /s/ George A. Scangos ---------------------------------- George A. Scangos, Ph.D. President and Chief Executive Officer POWER OF ATTORNEY KNOW ALL PERSONS BY THESE PRESENTS, that each person whose signature appears below constitutes and appoints George A. Scangos and Frank Karbe, and each or any one of them, his true and lawful attorney-in-fact and agent, with full power of substitution and resubstitution, for him and in his name, place and stead, in any and all capacities, to sign any and all amendments (including post-effective amendments) to this Registration Statement, and to file the same, with all exhibits thereto, and other documents in connection therewith, with the Securities and Exchange Commission, granting unto said attorneys-in-fact and agents, and each of them, full power and authority to do and perform each and every act and thing requisite and necessary to be done in connection therewith, as fully to all intents and purposes as he might or could do in person, hereby ratifying and confirming all that said attorneys-in-fact and agents, or any of them, or their or his substitutes or substitute, may lawfully do or cause to be done by virtue hereof. Pursuant to the requirements of the Securities Act of 1933, as amended, this Registration Statement has been signed by the following persons in the capacities and on the dates indicated. Signature Title Date - ------------------------------ ---------------------------------- ------------------ /s/ George A. Scangos President, Chief Executive March 10, 2004 - ------------------------------ Officer and Director George A. Scangos, Ph.D. (Principal Executive Officer) /s/ Frank Karbe Chief Financial Officer March 10, 2004 - ------------------------------ (Principal Financial and Frank Karbe Accounting Officer) /s/ Stelios Papadopoulos Chairman of the Board of - ------------------------------- Directors March 10, 2004 Stelios Papadopoulos, Ph.D. /s/ Charles Cohen Director March 10, 2004 - ------------------------------ Charles Cohen, Ph.D. /s/ Jason Fisherman Director March 10, 2004 - ------------------------------- Jason S. Fisherman, M.D. /s/ Jean-Francois Formela Director March 10, 2004 - ------------------------------- Jean-Francois Formela, M.D. /s/ Vincent T. Marchesi Director March 10, 2004 - ------------------------------- Vincent T. Marchesi, Ph.D. /s/ Frank McCormick Director March 10, 2004 - ------------------------------- Frank McCormick, Ph.D. /s/ Lance Willsey Director March 10, 2004 ------------------------------ Lance Willsey, M.D. /s/ Jack L. Wyszomierski Director March 10, 2004 - ------------------------------- Jack L. Wyszomierski

EXHIBIT INDEX Exhibit Number Description 4.1 Specimen Common Stock Certificate. (1) 4.2 Fourth Amended and Restated Registration Rights Agreement, dated February 26, 1999 among Exelixis, Inc. and Certain Stockholders of Exelixis,Inc. (1) 4.3 Warrant, dated August 17, 1998, to purchase 125,796 post-split shares of Exelixis, Inc. Series A preferred stock in favor of Comdisco, Inc. (1) 4.4 Warrant, dated August 17, 1998, to purchase 15,365 post-split shares of Exelixis, Inc. Series A preferred stock in favor of Greg Stento. (1) 4.5 Warrant, dated January 24, 1996, to purchase 267,857 post-split shares of Exelixis, Inc. Series B convertible stock in favor of MMC/GATX Partnership No. 1. (1) 4.6 Warrant, dated September 25, 1997, to purchase 63,750 post-split shares of Exelixis, Inc. common stock in favor of MMC/GATX Partnership No. 1. (1) 4.7 Warrant, dated November 15, 1999, to purchase 9,000 post-split shares of Exelixis, Inc. common stock in favor Bristow Investments, L.P. (1) 4.8 Warrant, dated November 15, 1999, to purchase 101,250 post-split shares of Exelixis, Inc. common stock in favor of Slough Estates USA, Inc. (1) 4.9 Warrant, dated November 15, 1999, to purchase 2,250 post-split shares of Exelixis, Inc. common stock in favor of Laurence and Magdalena Shushan Trust. (1) 4.10 Warrant, dated April 1, 2000, to purchase 70,875 shares of Exelixis, Inc. common stock in favor of Slough Estates USA, Inc. (2) 4.11 Warrant, dated April 1, 2000, to purchase 6,300 shares of Exelixis, Inc. common stock in favor of Bristow Investments, L.P. (2) 4.12 Warrant, dated April 1, 2000, to purchase 1,575 shares of Exelixis, Inc. common stock in favor of Laurance and Madgalena Shusan Family Trust. (2) 4.13 Form of Convertible Promissory Note, dated May 22, 2001 by and between Exelixis, Inc. and Protein Design Labs, Inc. (3) 4.14 Form of Note Purchase Agreement, dated May 22, 2001 by and between Exelixis, Inc. and Protein Design Labs, Inc. (3) 5.1 Opinion of Cooley Godward LLP. 23.1 Consent of Ernst & Young LLP, Independent Auditors. 23.2 Consent of Cooley Godward LLP (contained in Exhibit 5.1 to this Registration Statement). 24.1 Power of Attorney (contained on the signature pages to this Registration Statement). 99.1 2000 Equity Incentive Plan. (1) 99.2 2000 Employee Stock Purchase Plan. (1) ________________________ (1) Filed as an Exhibit to Exelixis, Inc.'s Registration Statement on Form S-1, as amended (File No. 333-30978), as filed with the Securities and Exchange Commission on February 7, 2000, as amended, and incorporated herein by reference. (2) Filed as an Exhibit to Exelixis, Inc.'s Quarterly Report on Form 10-Q for the quarter ended March 31, 2000, filed with the Securities and Exchange Commission on May 15, 2000 and incorporated herein by reference. (3) Filed as an Exhibit to Exelixis, Inc.'s Quarterly Report on Form 10-Q for the quarter ended June 30, 2001, as filed with the Securities and Exchange Commission on August 14, 2001 and incorporated herein by reference.

                                                                     EXHIBIT 5.1


                                                           Robert L. Jones, Esq.
                                                                  (650) 843-5034
                                                              jonesrl@cooley.com


March 10, 2004


Exelixis, Inc.
170 Harbor Way
P.O. Box 511
South San Francisco, CA 94083


Ladies  and  Gentlemen:

You  have  requested  our  opinion with respect to certain matters in connection
with the filing by Exelixis, Inc. (the "Company") of a Registration Statement on
Form  S-8  (the  "Registration  Statement")  with  the  Securities  and Exchange
Commission  covering  the  offering  of  an aggregate of 1,599,429 shares of the
Company's  common  stock,  $.001  par  value  (the  "Shares"),  pursuant  to the
Company's  2000  Equity  Incentive  Plan  and  2000 Employee Stock Purchase Plan
(collectively  the  "Plans").

In connection with this opinion, we have examined the Registration Statement and
related  Prospectuses,  the  Company's  Amended  and  Restated  Certificate  of
Incorporation  and  Restated  Bylaws, as currently in effect, the Plans and such
other  documents,  records,  certificates, memoranda and other instruments as we
deem necessary as a basis for this opinion.  We have assumed the genuineness and
authenticity  of  all  documents submitted to us as originals, the conformity to
originals  of  all  documents  submitted  to  us  as  copies thereof and the due
execution  and  delivery of all documents where due execution and delivery are a
prerequisite  to  the  effectiveness  thereof.

On  the  basis  of the foregoing, and in reliance thereon, we are of the opinion
that  the  Shares,  when  sold  and  issued  in  accordance  with the Plans, the
Registration Statement and the related Prospectus, will be validly issued, fully
paid  and nonassessable (except as to shares issued pursuant to certain deferred
payment  arrangements,  which  will  be  fully  paid and nonassessable when such
deferred  payments  are  made  in  full).

We  consent  to  the  filing  of  this opinion as an exhibit to the Registration
Statement.

Very  truly  yours,

Cooley  Godward  LLP


By:     /s/ Robert L. Jones
        ----------------------
            Robert L. Jones


                                                                    Exhibit 23.1


               CONSENT OF ERNST & YOUNG LLP, INDEPENDENT AUDITORS

We consent to the incorporation by reference in the Registration Statement (Form
S-8)  pertaining  to  the 2000 Equity Incentive Plan and the 2000 Employee Stock
Purchase  Plan  of  Exelixis,  Inc.  of  our report dated January 30, 2004, with
respect  to  the consolidated financial statements of Exelixis, Inc. included in
its  Annual  Report (Form 10-K) for the year ended December 31, 2003, filed with
the  Securities  and  Exchange  Commission.

                                                           /s/ Ernst & Young LLP

Palo Alto, California
March 8, 2004