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UNITED STATES
SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549
    FORM 10-K/A (Amendment No. 1)
    (X)
    
    ANNUAL REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934
 For the Fiscal Year ended December 31, 2003 Commission File Number 000-27765 SYMYX TECHNOLOGIES, INC.  Delaware
    
    77-0397908(State or other jurisdiction of
    
    (IRS Employerincorporation or organization)
    
    Identification Number)3100 Central Expressway,Santa Clara, California 95051
    
    (408) 764-2000(Address of principal executive offices including zip code)
    
    (Registrants telephone number,including area code)
 SECURITIES REGISTERED PURSUANT TO SECTION 12(b) OF THE ACT:
None SECURITIES REGISTERED PURSUANT TO SECTION 12(g) OF THE ACT:
Common Stock, $0.001 Par Value Indicate by check mark whether the registrant (1) has filed all reports
required to be filed by Section 13 or 15(d) of the Securities Exchange Act of
1934 during the preceding 12 months (or for such shorter period that the
registrant was required to file such reports), and (2) has been subject to such
filing requirements for the past 90 days. Yes x  No o Indicate by check mark if disclosure of delinquent filers pursuant to Item
405 of Regulation S-K is not contained herein, and will not be contained, to
the best of registrants knowledge, in definitive proxy or information
statements incorporated by reference in Part III of this Form 10-K or any
amendment to this Form 10-K. o Indicate by check mark whether the registrant is an accelerated filer (as
defined in Exchange Act Rule 12b-2). Yes x  No o The approximate aggregate market value of the registrants common stock
held by non-affiliates as of June 30, 2003 (the last business day of the
registrants most recently completed second fiscal quarter) was $512,194,967,
based on the closing price for the common stock on the Nasdaq National Market
on such date. As of March 1, 2004, 31,820,271 shares of Common Stock were outstanding. DOCUMENTS INCORPORATED BY REFERENCE Certain sections of the Proxy Statement to be filed in connection with the
2004 Annual Meeting of Stockholders are incorporated by reference into Part III
of thisForm 10-KReport where indicated. EXPLANATORY NOTE Symyx Technologies, Inc. amends its Annual Report on Form 10-K for the
fiscal year ended December 31, 2003 (filed on March 8, 2004), as set forth in
this Form 10-K/A (Amendment No. 1), solely to replace the certifications of its
chief executive officer and chief financial officer filed in the original Form
10-K as exhibits 31.1 and 31.2 with the new certifications specified in the
rules and regulations of the Securities Exchange Commission pursuant to Section
302(a) of the Sarbanes-Oxley Act of 2002. This Form 10-K/A does not reflect
events occurring after the filing of the original Form 10-K, or modify or
update the disclosures therein in any way other than as required to reflect the
amendment described above.




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TABLE OF CONTENTS  SIGNATURESEXHIBIT INDEXEXHIBIT 31.1EXHIBIT 31.2    Table of Contents  
 SIGNATURES Pursuant to the requirements of the Securities Exchange Act of 1934, the
Registrant has duly caused this report to be signed on its behalf by the
undersigned, thereunto duly authorized.  SYMYX TECHNOLOGIES, INC.(Registrant)Date: April 15, 2004/s/ Steven D. GoldbySteven D. GoldbyChairman of the Board,Chief Executive Officer(Principal Executive Officer)Date: April 15, 2004/s/ Jeryl L. HillemanJeryl L. HillemanSenior Vice President,Chief Financial Officer(Principal Financial and Accounting Officer)
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EXHIBIT INDEX ExhibitNumber
    
    
    
    Description of Document3.1
    
    (1)
    
    Amended and Restated Certificate of Incorporation3.2
    
    (7)
    
    Amended Bylaws of Symyx4.1
    
    (2)
    
    Specimen Common Stock Certificate5.1
    
    (2)
    
    Opinion of Wilson Sonsini Goodrich & Rosati, Professional Corporation10.1
    
    (2)
    
    Restated Investors Rights Agreement dated March 27, 199810.2
    
    (2)
    
    1996 Stock Plan and forms of agreements thereunder10.3
    
    (2)
    
    1997 Stock Plan and forms of agreements thereunder10.4
    
    (2)
    
    1999 Employee Stock Purchase Plan10.5
    
    (2)
    
    Form of Director and Executive Officer Indemnification Agreement10.6
    
    (2)
    
    Form of Change of Control Agreement between Symyx and the following
individuals: Steven D. Goldby, Isy Goldwasser, Jeryl L. Hilleman, and
W. Henry Weinberg10.7
    
    (2)
    
    Standard Industrial/Commercial Single-Tenant Lease dated November 15,
1996 between Symyx and Patrick and Bette Ng, Co-Trustees for The Ng
Living Trust, for office space located at 3100 Central Expressway,
Santa Clara, California, and addenda and inserts thereto10.7(a)
    
    (2)
    
    First Amendment to Lease between Symyx and Patrick and Bette Ng,
Co-Trustees for The Ng Living Trust10.8
    
    (2)
    
    Collaboration Agreement dated March 1, 1998 between Symyx and Bayer AG10.8(a)
    
    (2)
    
    Amendment No. 1 dated May 1, 1998 to Collaboration Agreement between
Symyx and Bayer AG10.8(b)
    
    (2)
    
    Amendment No. 2 dated November 1, 1998 to Collaboration Agreement
between Symyx and Bayer AG10.8(c)
    
    (2)
    
    Amendment No. 3 dated January 1, 1999 to Collaboration Agreement
between Symyx and Bayer AG10.8(d)
    
    (2)
    
    Amendment No. 4 dated September 15, 1999 to Collaboration Agreement
between Symyx and Bayer AG10.9
    
    (2)
    
    Celanese-Symyx Collaboration Agreement dated August 1, 1998 between
Symyx and Celanese Ltd.10.10
    
    (2)
    
    Collaborative Research and License Agreement dated January 1, 1999
between Symyx and The Dow Chemical Company10.11
    
    (2)
    
    License Agreement dated June 22, 1995 between Symyx and Lawrence
Berkeley Laboratory, on behalf of The Regents of the University of
California10.12
    
    (2)
    
    License and Supply Agreement effective August 6, 1999 between Symyx
and Argonaut Technologies, Inc.10.13
    
    (3)
    
    Lease by and between East Arques Sunnyvale, LLC and Symyx
Technologies, Inc. for the premises at 1263 E. Arques, Sunnyvale,
California, and addenda and inserts thereto10.14
    
    (4)
    
    2001 Nonstatutory Stock Option Plan*10.15
    
    (5)
    
    License Agreement dated February 21, 2003 between Symyx Technologies,
Inc. and Symyx Therapeutics, Inc.*10.16
    
    (6)
    
    Alliance, Technology Transfer, and License Agreement effective April
1, 2003 between Symyx Technologies, Inc., Symyx Discovery Tools, Inc.
and ExxonMobil Research and Engineering Company.14
    
    (7)
    
    Symyx Technologies, Inc. Code of Conduct and Ethics21
    
    (7)
    
    List of Subsidiaries23.1
    
    (7)
    
    Consent of Ernst & Young LLP, Independent Auditors31.1
    
    (8)
    
    Certification of Chief Executive Officer pursuant to Rules 13a-14(a)
and 15d-14(a) promulgated under the Securities Exchange Act of 1934,
as amended, as adopted pursuant to Section 302(a) of the
Sarbanes-Oxley Act of 2002.31.2
    
    (8)
    
    Certification of Chief Financial Officer pursuant to Rules 13a-14(a)
and 15d-14(a) promulgated under the Securities Exchange Act of 1934,
as amended, as adopted pursuant to Section 302(a) of the
Sarbanes-Oxley Act of 2002.32.1
    
    (7)
    
    Certification of Chief Executive Officer and Chief Financial Officer pursuant to 18 U.S.C. Section 1350, as adopted pursuant to Section 906 of the Sarbanes-Oxley Act of 2002.
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* Confidential treatment has been requested for portions of these exhibits.   (1)
    
    Incorporated by reference to the same number exhibit filed with Registrants Quarterly Report on Form 10-Q for the period ended June 30, 2003.(2)
    
    Incorporated by reference to the same number exhibit filed with Registrants Registration Statement on Form S-1 (File No. 333-87453), as amended.(3)
    
    Incorporated by reference to the same number exhibit filed with Registrants Annual Report on Form 10-K for the year ended December 31, 2000.(4)
    
    Incorporated by reference to exhibit 4.1 filed with Registrants Registration Statement on Form S-8 (File No. 333-82166).(5)
    
    Incorporated by reference to the same number exhibit filed with Registrants Quarterly Report on Form 10-Q for the period ended June 30, 2003.(6)
    
    Incorporated by reference to the same number exhibit filed with Registrants Quarterly Report on Form 10-Q for the period ended September 30, 2003.(7)
    
    Incorporated by reference to the same number exhibit filed with Registrants Annual Report on Form 10-K for the year ended December 31, 2003.(8)
    
    Filed herewith. 4