UNITED STATES SECURITIES AND
    EXCHANGE COMMISSIONWashington, D.C.
    20549
      
 Form 10-K/A(Amendment No. 1)
 
  ANNUAL
    REPORT PURSUANT TO SECTION 13 OR 15(d) OF
    THE SECURITIES EXCHANGE ACT OF 1934
  For the
    fiscal year ended December 31, 2007
  Commission file number
    000-28401
  MAXYGEN,
    INC. (Exact
    name of registrant as specified in its charter)
  Delaware

77-0449487(State or other jurisdiction
    of
    incorporation or organization)

(I.R.S. Employer
    Identification No.)   515
    Galveston Drive
    Redwood City, California 94063 (Address
    of principal executive offices)
   Registrants telephone number, including area code:(650) 298-5300
      Securities registered pursuant to Section 12(b) of the
    Act:
  Title of Each Class

Name of Each Exchange on Which RegisteredCommon Stock, $0.0001 par value

The NASDAQ Stock Market LLC   Securities registered pursuant to Section 12(g) of the
    Act:
 None
      o þ
  o þ
  þ o
  Regulation S-K Form 10-K Form 10-K. þ
  Rule 12b-2
  Large accelerated
    filer o

Accelerated
    filer þ

Non-accelerated
    filer o
    (Do not check if a smaller reporting company)

Smaller reporting
    company o   Rule 12b-2 o þ




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EXPLANATORY NOTE:
 This amendment to the registrants Annual Report on Form 10-K for the year ended December 31, 2007,
originally filed with the Securities and Exchange Commission (SEC) on March 7, 2008 (the
Original Filing), is being filed solely to re-file Exhibits 10.19, 10.19.1 and 10.19.3 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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TABLE OF
    CONTENTS
 
  PART IVItem 15:

Exhibits, Financial Statement Schedules


1SIGNATURES


2 
 i




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PART IV  Item 15
    EXHIBITS,
    FINANCIAL STATEMENT SCHEDULES 
 
  Exhibits.
   1




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SIGNATURES      By: /s/  Russell
    J. Howard     
  
 2




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EXHIBIT INDEX
  Incorporation by Reference

FiledExhibit No.

Description of Exhibit

Form

SEC File No.

Exhibit

Filing Date

Herewith3
.1

Amended and Restated Certificate of Incorporation


10-Q



000-28401



3
.1


8/14/20003
.2

Amended and Restated Bylaws


8-K



000-28401



3
.1


9/07/20074
.1

Specimen Common Stock Certificate


S-1



333-89413



4
.1


11/22/1999*10
.1

Form of Executive Officer and Director


S-1



333-89413



10
.7


10/20/1999Indemnification Agreement*10
.2

Form of Executive Officer Change of Control Agreement


10-Q



000-28401



10
.1


8/14/2001*10
.2.1

Form of Amendment No. 1 to Executive Officer Change of
    Control Agreement


10-K



000-28401



10
.3


3/27/2003*10
.2.2

Form of Amendment No. 2 to Executive Officer Change of
    Control Agreement


8-K



000-28401



10
.3


6/30/2006*10
.3

1997 Stock Option Plan, as amended, with applicable option
    agreement


10-Q



000-28401



10
.1


8/14/2002*10
.4

Form of Amendment to Stock Option Agreements


8-K



000-28401



10
.2


6/30/2006*10
.5

1999 Nonemployee Directors Stock Option Plan, as amended, with
    applicable option agreement


10-Q



000-28401



10
.3


8/14/2001*10
.5

1999 Employee Stock Purchase Plan, as amended


10-K



000-28401



10
.11


3/21/2001*10
.6

2000 International Stock Option Plan, as amended, with
    applicable option agreement


10-K



000-28401



10
.6


3/25/200210
.7

2000 Non-Officer Stock Option Plan, as amended, with applicable
    option agreement


S-8



333-57486



99
.3


3/23/2001*10
.8

2006 Equity Incentive Plan (including related form of stock
    option agreement)


8-K



000-28401



10
.4


6/30/2006*10
.8.1

Form of Restricted Stock Unit Award Agreement under 2006 Equity
    Incentive Plan


S-8



333-138898



4
.2


11/22/200610
.9

Lease, dated as of October 21, 1998, between Metropolitan
    Life Insurance Company and Maxygen, Inc.


S-1



333-89413



10
.4


10/20/199910
.9.1

First Amendment to Lease, dated as of February 26, 1999, by
    and between Metropolitan Life Insurance Company and Maxygen, Inc.


S-1



333-89413



10
.5


10/20/199910
.9.2

Second Amendment to Lease, dated as of October 24, 2000, by
    and between Metropolitan Life Insurance Company and Maxygen, Inc.


10-K



000-28401



10
.6


3/21/200110
.9.3

Third Amendment to Lease, dated October 22, 2003, by and
    between Metropolitan Life Insurance Company and Maxygen, Inc.


10-K



000-28401



10
.15


3/12/2004 3




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Incorporation by Reference

FiledExhibit No.

Description of Exhibit

Form

SEC File No.

Exhibit

Filing Date

Herewith10
.9.4

Fourth Amendment to Lease dated December 15, 2004 by and
    between Metropolitan Life Insurance Company and Maxygen, Inc.


10-K



000-28401



10
.13


3/15/200510
.9.5

Fifth Amendment to Lease dated as of August 24, 2006, by
    and between Metropolitan Life Insurance Company and Maxygen, Inc.


8-K



000-28401



10
.2


8/25/200610
.10

Lease, dated December 15, 2004, between Metropolitan Life
    Insurance Company and Maxygen, Inc.


10-K



000-28401



10
.14


3/15/200510
.10.1

First Amendment to Lease, dated as of August 24, 2006, by
    and between Metropolitan Life Insurance Company and Maxygen, Inc.


8-K



000-28401



10
.1


8/25/200610
.11

Lease Agreement, dated May 5, 2000, between ProFound Pharma
    A/S and The Science Park in Horsholm


10-Q



000-28401



10
.1


11/14/200010
.12

Technology Transfer Agreement, dated March 14, 1997
    (effective March 1, 1998), among Maxygen, Inc., Affymax
    Technologies N.V. and Glaxo Group Limited, as amended


S-1



333-89413



10
.3


12/15/1999*10
.13

Description of 2006 Executive Officer Cash Bonus Plan


8-K



000-28401



10
.1


6/30/2006*10
.14

Letter Agreement (re tax equalization payments), dated
    November 20, 2006, between Elliot Goldstein and Maxygen,
    Inc.


10-K



000-28401



10
.25


3/14/200710
.15

Cross License Agreement, dated as of July 16, 2003, between
    Maxygen, Inc. and Amgen Mountain View Inc. 
    (as successor to Avidia, Inc.)


10-K



000-28401



10
.27


3/14/200710
.16+

Amended and Restated Exclusive License Agreement, dated
    July 10, 2006 (effective as of April 1, 2006), between
    Regents of the University of Minnesota and Maxygen, Inc.


10-Q



000-28401



10
.6


8/07/2006*10
.17

Consulting Agreement, between the Company and Waverley
    Associates, Inc., dated as of April 1, 2006


8-K



000-28401



10
.1


4/04/2006*10
.18

Consulting Agreement, between the Company and Michael Rabson,
    effective as of April 1, 2008


8-K



000-28401



10
.1


3/04/2008*10
.18.1

Letter Agreement (re extension of Consulting Agreement), between
    the Company and Waverley Associates, Inc., dated as of
    December 19, 200710
.19

License Agreement, dated as of March 28, 2002, between the
    Company and Codexis, Inc.


















X 
 4




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Incorporation by Reference

FiledExhibit No.

Description of Exhibit

Form

SEC File No.

Exhibit

Filing Date

Herewith10
.19.1

Amendment No. 1 to License Agreement, dated as of
    September 13, 2002, between the Company and Codexis, Inc.


















X10
.19.2

Amendment No. 2 to License Agreement, dated as of
    October 1, 2002, between the Company and Codexis, Inc.10
.19.3

Amendment No. 3 to License Agreement, dated as of
    August 22, 2006, between the Company and Codexis, Inc.


















X*10
.20

Description of Non-Employee Director Compensation21
.1

List of Subsidiaries23
.1

Consent of Independent Registered Public Accounting Firm24
.1

Power of Attorney (included on signature page)31
.1

Certification of Chief Executive Officer pursuant to
    Section 302 of the Sarbanes-Oxley Act of 2002


















X31
.2

Certification of Chief Financial Officer pursuant to
    Section 302 of the Sarbanes-Oxley Act of 2002


















X32
.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 granted, or 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. 
 5