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United StatesSecurities and Exchange Commission
 Washington, D.C. 20549
 
 Form 10-Q/A
 (Amendment No. 1)  QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(D) OF
THE SECURITIES EXCHANGE ACT OF 1934
 For the quarterly period ended June 30, 2008
 Commission file number 000-28401
 MAXYGEN, INC.
 (Exact name of registrant as specified in its charter)
 Delaware(State of incorporation)
    
    77-0449487(I.R.S. Employer Identification No.)
 515 Galveston Drive
Redwood City, California 94063  (Address of principal executive offices, including zip code)
 (650) 298-5300  (Registrants telephone number, including area code)
 
  þ o
  Large accelerated filer o
    
    Accelerated filer þ
    
    Non-accelerated filer o
    
    Smaller reporting company o(Do not check if a smaller reporting company)
  o þ




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EXPLANATORY NOTE:
 This amendment to
the registrants Quarterly Report on Form 10-Q for the quarter ended June 30, 2008,
originally filed with the Securities and Exchange Commission (SEC) on August 5, 2008
 (the Original Filing), is being filed solely to re-file Exhibits 2.1, 2.1.1
and 2.1.2 to include changes to the redactions in such exhibits, as compared to the versions
previously filed, made in response
to comments received from the staff of the SEC in connection with a confidential
treatment request.
 This amendment does not
reflect events occurring after the filing of the Original Filing, and is not intended
 to modify or update the disclosures therein or the exhibits
filed therewith in any way, except as specifically noted above.




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MAXYGEN, INC.
FORM 10-Q/A
QUARTER ENDED JUNE 30, 2008
  Item 6: Exhibits
    
    
    1SIGNATURES
    
    
    3EX-2.1EX-2.1.1EX-2.1.2EX-31.1EX-31.2




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Exhibits
  2.1
    
    Technology Transfer Agreement, dated as of July 1, 2008, by and among
Maxygen, Inc., Maxygen Holdings Ltd., Maxygen ApS and Bayer HealthCare LLC.2.1.1
    
    Intellectual Property Cross License Agreement, dated as of July 1, 2008, by and
among Maxygen, Inc., Maxygen Holdings Ltd., Maxygen ApS and Bayer HealthCare LLC.2.1.2
    
    License Agreement, dated as of July 1, 2008, by and between Maxygen, Inc. and Bayer
HealthCare LLC.10.1*
    
    Form of Amended and Restated Change of Control Agreement for Executive
Officers10.2*
    
    Letter Agreement, dated May 12, 2008, regarding amendment to Consulting
Agreement, dated April 1, 2006, between Maxygen, Inc. and Waverley Associates, Inc.31.1
    
    Certification of Chief Executive Officer pursuant to Section 302 of the
Sarbanes-Oxley Act of 2002




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31.2
    
    Certification of Chief Financial Officer pursuant to Section 302 of the
Sarbanes-Oxley Act of 200232.1
    
    Certification of Chief Executive Officer and Chief Financial Officer pursuant
to Section 906 of the Sarbanes-Oxley Act of 2002
 
 *
    
    Management contract or compensatory plan or arrangement.
    
    Confidential treatment has been  requested with respect to portions of the
exhibit. A complete copy of the agreement, including the redacted terms, has been separately
filed with the Securities and Exchange Commission.
    
    Previously filed or furnished with the Original Filing. 2




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Signatures
  MAXYGEN, INC.January 9, 2009
    By:
    /s/ Russell J. HowardRussell J. HowardChief Executive Officer 3