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.