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SECURITIES AND EXCHANGE COMMISSION


Washington, D.C. 20549





Form 10-K/A


(Amendment No. 1)




|  |                                                                                                                                                                                                             
|- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
|þ | ANNUAL REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE
    SECURITIES EXCHANGE ACT OF 1934 FOR THE YEAR ENDED
    DECEMBER 31, 2004.                                                                          
| 
|o | TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE
    SECURITIES EXCHANGE ACT OF 1934 FOR THE TRANSITION PERIOD
    FROM                                     TO                                     .

Commission File No. 0-28298





Onyx Pharmaceuticals, Inc.


(Exact name of registrant as specified in its charter)


|                                                                   |  |                                         
|------------------------------------------------------------------ |  | ----------------------------------------
|Delaware                                                           |  | 94-3154463                              
|(State or other jurisdiction of
    Incorporation or Organization) |  | (I.R.S. Employer
    Identification No.)

2100 Powell Street


Emeryville, California 94608


(510) 597-6500


(Address, including zip code, and telephone number,


including area code, of registrants principal executive
offices)


Securities Registered Pursuant to Section 12(b) of the
Act: None


Securities Registered Pursuant to Section 12(g) of the
Act:


|                              |  |                                          
|----------------------------- |  | -----------------------------------------
|Title of Each Class           |  | Name of Each Exchange on Which Registered
|                              |  |                                          
|Common Stock $0.001 par value |  | Nasdaq National Market                   




þ o


o


þ o














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|  |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
|- | --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
|* | Excludes 10,690,616 shares of Common Stock held by
    directors, officers and stockholders whose beneficial ownership
    exceeds 5% of the Registrants Common Stock outstanding.
    The number of shares owned by such persons was determined based
    upon information supplied by such persons and upon
    Schedules 13D and 13G, if any, filed with the SEC.
    Exclusion of shares held by any person should not be construed
    to indicate that such person possesses the power, direct or
    indirect, to direct or cause the direction of the management or
    policies of the Registrant, that such person is controlled by or
    under common control with the Registrant, or that such persons
    are affiliates for any other purpose.



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TABLE OF CONTENTS



|              |                                                                                               |  |  |  |  |  |  | 
|------------- | --------------------------------------------------------------------------------------------- |  |  |  |  |  |  | 
|              | Item 7. Managements Discussion and Analysis of Financial Condition and Results of Operations
|SIGNATURES   
|EXHIBIT INDEX
|Exhibit 31.2 



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EXPLANATORY NOTE






| |    |                                                                                                                                                                                         
| | -- | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
| | 1. | Part II, Item 7  Managements
    Discussion and Analysis of Financial Condition and Results of
    Operations  Results of Operations  General
    and Administrative Expenses; and
|
| | 2. | Part II, Item 7  Managements
    Discussion and Analysis of Financial Condition and Results of
    Operations  Income Taxes.                                                       



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|        |                                                                                          
|------- | -----------------------------------------------------------------------------------------
|Item 7. | Managements Discussion and Analysis of Financial
    Condition and Results of Operations

The following Managements Discussion and Analysis of
Financial Condition and Results of Operations contains
forward-looking statements that involve risks and uncertainties.
We use words such as may, will,
expect, anticipate,
estimate, intend, plan,
predict, potential, believe,
should and similar expressions to identify
forward-looking statements. These statements appearing
throughout our 10-K are statements regarding our intent, belief,
or current expectations, primarily regarding our operations. You
should not place undue reliance on these forward-looking
statements, which apply only as of the date of this Annual
Report on Form 10-K. Our actual results could differ
materially from those anticipated in these forward-looking
statements for many reasons, including those set forth under
Business and Additional Business Risks,
as well as those discussed elsewhere in this Annual Report on
Form 10-K.


Overview












Critical Accounting Policies and the Use of Estimates




1



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Stock based compensation:


Research and Development Expense:


Results of Operations




| |                                             
| | --------------------------------------------
| | Years Ended December 31, 2004, 2003 and 2002

Total Revenue.


Research and Development Expenses.


2



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|                                        |  |                                                                                                                          |      |          |  |                                                               |      |                      |      |   |      |   |      |      |  |   |      | 
|--------------------------------------- |  | ------------------------------------------------------------------------------------------------------------------------ | ---- | -------- |  | ------------------------------------------------------------- | ---- | -------------------- | ---- | - | ---- | - | ---- | ---- |  | - | ---- | 
|                                        |  |                                                                                                                          |      |          |  |                                                               |      | Research and         |     
|                                        |  |                                                                                                                          |      |          |  |                                                               |      | Development Expenses |     
|                                        |  |                                                                                                                          |      |          |  |                                                               |      | for the year ended   |     
|                                        |  |                                                                                                                          |      |          |  |                                                               |      | December 31,         |     
|                                        |  |                                                                                                                          |      | Collabo- |  | Phase of Development                                         |      |                      |     
|Product                                 |  | Description                                                                                                              |      | rator    |  | Estimated Completion                                          |      | 2004                 |      |   | 2003 |   |      | 2002 | 
|                                        |  |                                                                                                                          |      |          |  |                                                               |      |                      |      |   |      |   |      |      | 
|                                        |  |                                                                                                                          |      |          |  |                                                               |      | (In millions)        |     
|Sorafenib (1)                           |  | Small Molecule Inhibitor of tumor cell proliferation and
    angiogenesis, targeting RAF Kinase, VEGFR-2 and
    PDGFR-β |      | Bayer    |  | Phase I  2004
    Phase II  Unknown
    Phase III  Unknown |      | $                    | 33.4 |   |      | $ | 19.4 |      |  | $ | 11.8 | 
|Therapeutic Virus Programs (2)          |  | Programs discontinued during the second quarter of 2003. See
    Note 2 to our Financial Statements                      |      |         |  |                                                              |      |                      | 2.4  |   |      |   | 12.7 |      |  |   | 31.8 | 
|                                        |  |                                                                                                                          |      |          |  |                                                               |      |                      |      |   |      |   |      |      | 
|Total Research and Development Expenses |  | $                                                                                                                        | 35.8 |          |  | $                                                             | 32.1 |                      |      | $ | 43.6 |  
|                                        |  |                                                                                                                          |      |          |  |                                                               |      |                      |     






|    |                                                                                                                                                                       
|--- | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------
|(1) | Aggregate research and development costs-to-date through
    December 31, 2004 incurred by Onyx since fiscal year 2000
    for the sorafenib project is $72.7 million.

3



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|    |                                
|--- | -------------------------------
|(2) | Costs in 2004 were comprised of



| |    |                          
| | -- | -------------------------
| | a. | stock-based compensation;



| |    |                                                                                                                                                                                                              
| | -- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
| | b. | consulting fees for consultants retained in connection with the
    orderly wind-down of the virus programs and preservation of
    related assets for potential future divestiture or
    commercialization;



| |    |                                                                                                                                   
| | -- | ----------------------------------------------------------------------------------------------------------------------------------
| | c. | sponsored research at the University of California,
    San Francisco related to the preservation of the
    programs assets, and



| |    |                                                                                                        
| | -- | -------------------------------------------------------------------------------------------------------
| | d. | outside services related to stability testing and storage of
    virus product related to the programs.

Marketing Expenses.


General and Administrative Expenses.


Restructuring.




Interest Income and (Expense), Net.


4



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Other Expense  Related Party.


Other Income.


Income Taxes




Related Party Transactions










5



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Liquidity and Capital Resources












6



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|                                         |  |                        |       |           |        |   |     |       |  |     |       |  |       |         |       |  |  |   |     | 
|---------------------------------------- |  | ---------------------- | ----- | --------- | ------ | - | --- | ----- |  | --- | ----- |  | ----- | ------- | ----- |  |  | - | --- | 
|                                         |  | Payments Due by Period |      
|                                         |  |                        |      
|                                         |  |                        |       | Less than |        |   | 1-3 |       |  | 3-5 |       |  | After |        
|Contractual Obligations(1)               |  | Total                  |       |           | 1 Year |   |     | Years |  |     | Years |  |       | 5 Years |      
|                                         |  |                        |       |           |        |   |     |       |  |     |       |  |       |         |      
|                                         |  | (In thousands)         |      
|Operating leases, net of sublease income |  | $                      | 3,018 |           |        | $ | 639 |       |  | $   | 1,109 |  |       | $       | 1,164 |  |  | $ | 106 | 






|    |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
|--- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
|(1) | This table does not include any payments under research and
    development collaborations, as the amount and timing of such
    payments are not known. This table also does not include the
    obligation to repay the $20 million creditable
    milestone-based payments that we received from Bayer, because
    the repayment of these amounts is contingent upon Onyx
    generating profits or royalties on any products. Whether Onyx
    will ever generate any profits or royalties is not known at this
    time.



Recently Issued Accounting Standard






| |    |                                                                                                                                                                                                                                                                                                                                                                                                                       
| | -- | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
| | 1. | A modified prospective method in which compensation
    cost is recognized beginning with the effective date
    (a) based on the requirements of SFAS 123(R) for all
    share-based payments granted after the effective date and
    (b) based on the requirements of SFAS 123 for all
    awards granted to employees prior to the effective date of
    SFAS 123(R) that remain unvested on the effective date.
|
| | 2. | A modified retrospective method which includes the
    requirements of the modified prospective method described above,
    but also permits entities to restate based on the amounts
    previously recognized under SFAS 123 for purposes of pro
    forma disclosures either (a) all prior periods presented or
    (b) prior interim periods of the year of adoption.                                           



7



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SIGNATURES






| |                           
| | --------------------------
| | Onyx Pharmaceuticals, Inc.



| |     |                           
| | --- | --------------------------
| | By: | /s/ Hollings C.
    Renton

| |                                      
| | -------------------------------------
| | Hollings C. Renton                   
| | Chairman of the Board,               
| | President and Chief Executive Officer



|                                                                               |  |                                                                                                                  |  |                |  | 
|------------------------------------------------------------------------------ |  | ---------------------------------------------------------------------------------------------------------------- |  | -------------- |  | 
|Signature                                                                      |  | Title                                                                                                            |  | Date          
|                                                                               |  |                                                                                                                  |  |               
|                                                                              
|/s/ Hollings C. RentonHollings
    C. Renton                                   |  | Chairman of the Board,
    President and Chief Executive Officer
    (Principal Executive and Financial Officer) |  | March 24, 2005
|                                                                              
|/s/ Marilyn E. WortzmanMarilyn
    E. Wortzman                                 |  | Vice President, Finance and Administration
    (Principal Accounting Officer)                                    |  | March 24, 2005
|                                                                              
|*Paul
    Goddard                                                              |  | Director                                                                                                         |  | March 24, 2005
|                                                                              
|*Antonio
    Grillo-López                                                      |  | Director                                                                                                         |  | March 24, 2005
|                                                                              
|*Magnus
    Lundberg                                                           |  | Director                                                                                                         |  | March 24, 2005
|                                                                              
|*Nicole
    Vitullo                                                            |  | Director                                                                                                         |  | March 24, 2005
|                                                                              
|*Wendell
    Wierenga                                                          |  | Director                                                                                                         |  | March 24, 2005
|                                                                              
|*Thomas
    G. Wiggans                                                         |  | Director                                                                                                         |  | March 24, 2005
|                                                                              
|*By:/s/ Hollings C.
    RentonHollings
    C.
    Renton,     Attorney-in-fact |  |                                                                                                                  |  |               

8



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EXHIBIT INDEX


|        |            |   |                         |                                                                                                                                                                                                                                                                                                                            
|------- | ---------- | - | ----------------------- | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
|Exhibit |            |   |                        
|Number  |            |   | Description of Document
|        |            |   |                        
|        | 3.1(1)     |   |                         | Restated Certificate of Incorporation of the Company.                                                                                                                                                                                                                                                                      
|       
|        | 3.2(1)     |   |                         | Bylaws of the Company.                                                                                                                                                                                                                                                                                                     
|       
|        | 3.3(2)     |   |                         | Certificate of Amendment to Amended and Restated Certificate of
    Incorporation.                                                                                                                                                                                                                                         
|       
|        | 4.1(1)     |   |                         | Reference is made to Exhibits 3.1, 3.2 and 3.3.                                                                                                                                                                                                                                                                            
|       
|        | 4.2(1)     |   |                         | Specimen Stock Certificate.                                                                                                                                                                                                                                                                                                
|       
|        | 4.4(1)     |   |                         | Amended and Restated Information and Registration Rights
    Agreement dated May 30, 1994 and as amended through
    May 16, 1995.                                                                                                                                                                                         
|       
|        | 10.1(1)*   |   |                         | Collaboration Agreement between Bayer Corporation (formerly
    Miles, Inc.) and the Company dated April 22, 1994.                                                                                                                                                                                                         
|       
|        | 10.1(i)(1) | * |                         | Amendment to Collaboration Agreement between Bayer Corporation
    and the Company dated April 4, 1996.                                                                                                                                                                                                                    
|       
|        | 10.2(1)*   |   |                         | Research, Development and Marketing Collaboration Agreement
    between Warner-Lambert Company and the Company, dated
    May 2, 1995.                                                                                                                                                                                     
|       
|        | 10.2(i)(1) |   |                         | Waiver of Certain Rights under the Research, Development and
    Marketing Agreement by Warner-Lambert Company dated as of
    March 28, 1996.                                                                                                                                                                             
|       
|        | 10.5(4)*   |   |                         | Technology Transfer Agreement dated April 24, 1992 between
    Chiron Corporation and the Company, as amended in the Chiron
    Onyx HPV Addendum dated December 2, 1992, in the Amendment
    dated February 1, 1994, in the Letter Agreement dated
    May 20, 1994 and in the Letter Agreement dated
    March 29, 1996.
|       
|        | 10.6(1)    |   |                         | Scientific Advisory Board Consulting Agreement between
    Dr. Frank McCormick and the Company, as of March 29,
    1996.                                                                                                                                                                                                  
|       
|        | 10.6(i)(1) |   |                         | Letter Agreement for Consulting Services between Dr. Frank
    McCormick and the Company dated April 17, 1996.                                                                                                                                                                                                             
|       
|        | 10.9(1)+   |   |                         | Letter Agreement between Dr. Gregory Giotta and the Company
    dated May 26, 1995.                                                                                                                                                                                                                                        
|       
|        | 10.13(1)+  |   |                         | 1996 Equity Incentive Plan.                                                                                                                                                                                                                                                                                                
|       
|        | 10.14(1)+  |   |                         | 1996 Non-Employee Directors Stock Option Plan.                                                                                                                                                                                                                                                                            
|       
|        | 10.15(1)+  |   |                         | 1996 Employee Stock Purchase Plan.                                                                                                                                                                                                                                                                                         
|       
|        | 10.16(3)   |   |                         | Lease by and between Hall Properties, Inc. and the Company dated
    September 9, 1992, the First Amendment thereto dated
    April 21, 1993 and the Second Amendment thereto dated
    May 11, 1996.                                                                                                                      
|       
|        | 10.17(1)+  |   |                         | Form of Indemnity Agreement to be signed by executive officers
    and directors of the Company.                                                                                                                                                                                                                           
|       
|        | 10.19(5)   |   |                         | Letter Agreement between Dr. Allan Balmain and the Company
    dated August 26, 1996, as amended March 13, 1997.                                                                                                                                                                                                           
|       
|        | 10.20(6)*  |   |                         | Amended and restated Research, Development and Marketing
    Collaboration Agreement dated May 2, 1995 between the
    Company and Warner-Lambert Company.                                                                                                                                                                 
|       
|        | 10.21(6)*  |   |                         | Research, Development and Marketing Collaboration Agreement
    dated July 31, 1997 between the Company and Warner-Lambert
    Company.                                                                                                                                                                                    
|       
|        | 10.23(6)*  |   |                         | Amendment to the Amended and Restated Research, Development and
    Marketing Collaboration Agreement, dated December 15, 1997,
    between the Company and Warner-Lambert Company.                                                                                                                                        
|       
|        | 10.24(7)*  |   |                         | Amendment to Collaboration Agreement between Bayer Corporation
    and the Company dated February 1, 1999.                                                                                                                                                                                                                 
|       
|        | 10.25(8)   |   |                         | Scientific Advisory Board Consulting Agreement effective
    September 10, 1999 between Allan Balmain and the Company
    including the First Amendment to Deed of Trust and Second
    Amended and Restated Promissory Note.                                                                                              
|       
|        | 10.26(9)*  |   |                         | Collaboration Agreement between the Company and Warner-Lambert
    Company dated October 13, 1999 and effective
    September 1, 1999.                                                                                                                                                                                     



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|        |            |  |                         |                                                                                                                                                                          
|------- | ---------- |  | ----------------------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------
|Exhibit |            |  |                        
|Number  |            |  | Description of Document
|        |            |  |                        
|       
|        | 10.27(9)   |  |                         | Stock Put and Purchase Agreement between the Company and
    Warner-Lambert Company dated October 13, 1999 and effective
    September 1, 1999.                          
|       
|        | 10.28(9)   |  |                         | Stock Purchase Agreement between the Company and the investors
    dated January 18, 2000.                                                                               
|       
|        | 10.29(10)  |  |                         | Third Amendment to Lease by and between the Metcalf Family
    Living Trust Dated June 11, 1993 and the Company effective
    February 24, 2000.                         
|       
|        | 10.31(6)*  |  |                         | Second Amendment to the Amended and Restated Research,
    Development and Marketing Agreement between Warner-Lambert and
    the Company dated May 2, 1995.             
|       
|        | 10.32(6)*  |  |                         | Second Amendment to Research, Development and Marketing
    Collaboration Agreement between Warner-Lambert and the Company
    dated July 31, 1997.                      
|       
|        | 10.33(11)+ |  |                         | Employment Offer Letter between Leonard E. Post, Ph.D. and
    the Company dated July 28, 2000.                                                                          
|       
|        | 10.34(12)* |  |                         | Process Development and Manufacturing Agreement between XOMA
    (US) LLC and Onyx Pharmaceuticals, Inc., dated January 29,
    2001.                                    
|       
|        | 10.35(13)+ |  |                         | Form of Executive Change in Control Severance Benefits Agreement.                                                                                                        
|       
|        | 10.36(14)* |  |                         | Amendment #1 to the Collaboration Agreement between the
    Company and Warner-Lambert dated August 6, 2001.                                                             
|       
|        | 10.37(14)* |  |                         | Amendment #3 to the Research, Development and Marketing
    Collaboration Agreement between the Company and Warner-Lambert
    dated August 6, 2001.                     
|       
|        | 10.38(14)* |  |                         | Amendment #3 to the Amended and Restated Research,
    Development and Marketing Collaboration Agreement between the
    Company and Warner-Lambert dated August 6, 2001.
|       
|        | 10.39(15)  |  |                         | Stock and Warrant Purchase Agreement between the Company and the
    investors dated May 6, 2002.                                                                        
|       
|        | 10.40(16)* |  |                         | Amendment No. 1 to the Process Development and
    Manufacturing Agreement between the Company and XOMA (US) LLC
    dated April 15, 2002.                               
|       
|        | 10.41(17)* |  |                         | Amendment to the Collaboration Agreement between the Company and
    Warner-Lambert Company dated September 16, 2002.                                                    
|       
|        | 10.42(18)  |  |                         | Stock Purchase Agreement between the Company and the investors
    dated February 13, 2003.                                                                              
|       
|        | 10.43(19)  |  |                         | Sublease between the Company and Siebel Systems dated
    August 5, 2004.                                                                                                
|       
|        | 23.1**     |  |                         | Consent of Independent Registered Public Accounting Firm.                                                                                                                
|       
|        | 24.1**     |  |                         | Power of Attorney. Reference is made to the signature page.                                                                                                              
|       
|        | 31.1**     |  |                         | Certification required by Rule 13a-14(a) or Rule 15d-14(a).                                                                                                              
|       
|        | 31.2       |  |                         | Certification required by Rule 13a-14(a) or Rule 15d-14(a).                                                                                                              
|       
|        | 32.1**     |  |                         | Certifications required by Rule 13a-14(b) or Rule 15d-14(b) and
    Section 1350 of Chapter 63 of Title 18 of the
    United States Code (18 U.S.C. 1350).               






| |   |                                                                            
| | - | ---------------------------------------------------------------------------
| | * | Confidential treatment has been received for portions of this
    document.



| |    |                  
| | -- | -----------------
| | ** | Previously filed.





|    |                                                                                                          
|--- | ---------------------------------------------------------------------------------------------------------
|(1) | Filed as an exhibit to Onyxs Registration Statement on
    Form SB-2 (No. 333-3176-LA).                 
|   
|(2) | Filed as an exhibit to Onyxs Quarterly Report on
    Form 10-Q for the quarter ended June 30, 2000.     
|   
|(3) | Filed as an exhibit to Onyxs Quarterly Report on
    Form 10-Q for the quarter ended June 30, 1996.     
|   
|(4) | Filed as an exhibit to Onyxs Annual Report on
    Form 10-K for the year ended December 31, 2001.       
|   
|(5) | Filed as an exhibit to Onyxs Quarterly Report on
    Form 10-Q for the quarter ended March 31, 1997.    
|   
|(6) | Filed as an exhibit to Onyxs Annual Report on
    Form 10-K for the year ended December 31, 2002.       
|   
|(7) | Filed as an exhibit to Onyxs Quarterly Report on
    Form 10-Q for the quarter ended March 31, 1999.    
|   
|(8) | Filed as an exhibit to Onyxs Quarterly Report on
    Form 10-Q for the quarter ended September 30, 1999.
|   
|(9) | Filed as an exhibit to Onyxs Current Report on
    Form 8-K filed on March 1, 2000.                     



|     |                                                                                                   
|---- | --------------------------------------------------------------------------------------------------
|(10) | Filed as an exhibit to Onyxs Annual Report on
    Form 10-K for the year ended December 31, 1999.



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|     |                                                                                                               
|---- | --------------------------------------------------------------------------------------------------------------
|(11) | Filed as an exhibit to Onyxs Quarterly Report on
    Form 10-Q for the quarter ended September 30, 2000.     
|    
|(12) | Filed as an exhibit to Onyxs Current Report on
    Form 8-K filed on February  23, 2001.                     
|    
|(13) | Filed as an exhibit to Onyxs Quarterly Report on
    Form 10-Q for the quarter ended March 31, 2001.         
|    
|(14) | Filed as an exhibit to Onyxs Quarterly Report on
    Form 10-Q for the quarter ended September 30, 2001.     
|    
|(15) | Filed as an exhibit to Onyxs Registration Statement on
    Form S-3 filed on June 5, 2002 (No. 333-89850).   
|    
|(16) | Filed as an exhibit to Onyxs Quarterly Report on
    Form 10-Q for the quarter ended June 30, 2002.          
|    
|(17) | Filed as an exhibit to Onyxs Quarterly Report on
    Form 10-Q for the quarter ended September 30, 2002.     
|    
|(18) | Filed as an exhibit to Onyxs Registration Statement on
    Form S-3 filed on March 25, 2003 (No. 333-104025).
|    
|(19) | Filed as an exhibit to Onyxs Quarterly Report on
    Form 10-Q for the quarter ended September 30, 2004.