##### Table of Contents



UNITED STATES SECURITIES AND
    EXCHANGE COMMISSION
 Washington, 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, 2006
  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
  o þ o
  Rule 12b-2 o þ
      DOCUMENTS INCORPORATED BY REFERENCE




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##### 



TABLE OF
    CONTENTS
  
  Part IItem 1:


Business


1Part IVItem 15:


Exhibits, Financial
    Statement Schedules


15SIGNATURES


18EXHIBIT 31.1EXHIBIT 31.2     i




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EXPLANATORY
    NOTE:
  This amendment to the registrants Annual Report on Form
    10-K for the
    year ended December 31, 2006, originally filed with the
    Securities and Exchange Commission (SEC) on
    March 14, 2007, is being filed solely to supplement
    disclosure in Item 1 of Part I of the original Form
    10-K under
    the caption Other Assets and Areas of Research 
    Investment in Avidia Inc. regarding the terms of the Cross
    License Agreement, dated as of July 16, 2003, between
    Maxygen, Inc. and Amgen Mountain View Inc. (as successor to
    Avidia, Inc.), which was filed as Exhibit 10.27 to the
    original Form
    10-K. This
    amendment is being filed in connection with the resolution of
    comments received from the SEC regarding an application for
    confidential treatment of the Cross License Agreement. This
    amendment does not reflect events occurring after the filing of
    the original Form
    10-K, and is
    not intended to modify or update the disclosures therein in any
    way, except as specifically noted above.
  Forward
    Looking Statements
    
    our ability to develop products suitable for commercialization;
    our predicted development and commercial timelines for any of
    our potential products, including the timing of any commencement
    of clinical trials of any product candidate and the progress of
    such clinical trials;
    our liquidity and future financial performance;
    the establishment, development and maintenance of any
    manufacturing or collaborative relationships;
    the effectiveness of our MolecularBreeding directed evolution
    platform and other technologies and processes;
    our ability to protect our intellectual property portfolio and
    rights;
    our ability to identify and develop new potential products;
    the attributes of any products we may develop; and
    our business strategies and plans.     ii




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PART I  Item 1
    BUSINESS  Overview
    
    MAXY-G34, a granulocyte colony stimulating factor, or G-CSF, for
    the treatment of neutropenia;
    MAXY-alpha, an interferon alpha product for the treatment of
    hepatitis C virus, or HCV, infection;
    MAXY-VII, a factor VII product for the treatment of uncontrolled
    bleeding in trauma, intracerebral hemorrhage and other
    indications; and
    MAXY-gamma, an interferon gamma product for the treatment of
    idiopathic pulmonary fibrosis and other indications.  2006
    Highlights
    
    We initiated a Phase I clinical trial in the United States
    to evaluate Maxy-G34.
    F. Hoffmann-La Roche Ltd., or Roche, initiated a
    Phase Ia clinical trial in New Zealand to evaluate
    MAXY-alpha and we received a $2 million milestone payment
    from Roche for the commencement of the trial.
    We achieved a manufacturing process development milestone in our
    MAXY-VII program and received a $5 million milestone
    payment from Roche for the achievement of the milestone.
    We received a $17.8 million cash payment for our equity
    interests in Avidia, Inc., which was acquired by Amgen Inc.
    We expanded the scope of exclusive licenses previously granted
    to Codexis, Inc. to our MolecularBreeding directed evolution
    platform for certain applications relating to energy, including
    biofuels, in exchange for the right to receive a percentage of
    revenues received by Codexis for the sale of energy products and
    the use of processes in the energy field.  Business
    Strategy
    
    Advance the Development of Our Lead Product
    Candidates.  Our primary focus is the advancement
    of our lead product candidate, MAXY-G34, through clinical
    development. We initiated a Phase I clinical trial in the
    United States for our lead MAXY-G34 product candidate in the
    third quarter of 2006 and plan to commence Phase IIa
    clinical trials in the first half of 2007. Roche has an
    exclusive license to develop and commercialize our MAXY-alpha
    product candidates for the treatment of HCV infection. Roche
    initiated a Phase Ia clinical trial of MAXY-alpha in New
    Zealand at the end of 2006 and has informed us that a
    Phase Ib clinical trial of MAXY-alpha in HCV patients will
    begin in 2007. In December 2005, we entered into an agreement
    with Roche relating to the co-development and commercialization
    of our MAXY-VII product candidates for acute bleeding
    indications. In March 2007, we received notice from Roche that
    Roche has elected to terminate this agreement, effective
    April 12, 2007.
    Create Value with Improved Next-Generation Protein
    Drugs.  Our research and development efforts focus
    on seeking to make improved and proprietary versions of
    currently marketed therapeutic proteins that address significant
    market opportunities. We identify currently marketed or
    clinically validated protein products that require or could
    benefit from improvements to address existing medical needs in
    the treatment 1




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of disease and serious medical conditions, and use our
    proprietary MolecularBreeding directed molecular evolution
    platform and other technologies to improve these products. We
    commit resources to only those product candidates that we
    believe are commercially viable.  
    Increase Value, Reduce Risk.  By using our
    technologies to improve the properties of currently marketed or
    clinically validated therapeutic proteins that have significant
    commercial value, we believe we can potentially create novel and
    proprietary
    best-in-class
    products that take advantage of known utility, development paths
    and markets. We believe that this approach may result in reduced
    risk and enhanced chances of commercial success as compared to
    the development of novel pharmaceutical products directed at
    unvalidated targets.
    Establish a Portfolio of Next-Generation Therapeutic
    Proteins.  In addition to our existing product
    candidates, we have an ongoing discovery effort focused on
    next-generation protein or protein subunit pharmaceuticals. Our
    goal is to leverage discoveries in our research programs or
    in-licensed product candidates to extend and expand our product
    pipeline. By broadening our product portfolio, we hope to
    increase the probability of clinical and commercial success and
    reduce our exposure to the impact of any one product failure.
    Establish Strategic Collaborations to Advance our Product
    Pipeline and Leverage Our Development
    Resources.  Part of our strategy has been to
    establish strategic collaborations that enable us to retain a
    large portion of the eventual value from our product candidates.
    We may enter into strategic collaborations at various stages in
    our research and development process that will allow us to
    further diversify our product development risks, reduce costs,
    access the complementary skills and infrastructure possessed by
    our partners and accelerate the development and
    commercialization of our product candidates.
    Manage Our Financial Resources.  Fiscal
    discipline and pragmatic allocation of our resources are key
    components of our strategy. We focus our financial resources on
    those functions that should enhance our ability to generate
    improved next-generation product candidates and rapidly advance
    these new product candidates through pre-clinical and clinical
    development.  Product
    Pipeline
    Development

CommercializationProduct Candidate

Indication

Responsibilities

Rights

StatusMAXY-G34

Neutropenia

Maxygen

Maxygen

Phase I; plan to commence
    Phase IIa clinical trial in first half of 2007.MAXY-alpha

Hepatitis C

Roche

Roche

Phase Ia; Roche expects to
    commence a Phase Ib clinical trial in 2007.MAXY-VII

Uncontrolled bleeding

Maxygen*

Maxygen*

Pre-clinical**MAXY-gamma

Idiopathic Pulmonary Fibrosis

InterMune

InterMune

Pre-clinical     *
    
    Maxygen and Roche are currently parties to an agreement relating
    to the co-development and commercialization of our MAXY-VII
    product candidates for acute bleeding indications. On
    March 13, 2007, we received notice from Roche that Roche
    has elected to terminate this agreement, effective
    April 12, 2007. Upon termination of the agreement, all
    rights to our MAXY-VII product candidates will revert to Maxygen.**
    
    Pre-clinical means process development, product
    scale-up,
    formulation and further testing in animals, including
    toxicology, pharmacokinetics and pharmacodynamics. 2




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MAXY-G34
        Market Opportunity. G-CSF
  Development Status. follow-up 21-day
        MAXY-alpha
     3




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Market Opportunity.
  Development Status.
    MAXY-VII
       4




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Market Opportunity.
  Development Status.
      MAXY-gamma
        Market Opportunity.
  Development Status.
 5




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Other
    Assets and Areas of Research
    Vaccines
      Investment
    in Codexis, Inc.
    Investment
    in Avidia Inc.
   6




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CD-40 CTLA-4, IL-12 IL-23), TPO/IL3 TNF/IL-1. twenty-five country-by-country
    Our
    Technologies
  MolecularBreeding
   7




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The
    MolecularBreeding Directed Evolution Process
  
  Step One:
    DNAShuffling Recombination Technologies
      Step Two:
    MaxyScan Screening
   8




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Other
    Technologies
    Our
    Strategic Collaborations
  Roche
  MAXY-alpha.
 9




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MAXY-VII.
  InterMune
  MAXY-gamma.
  Intellectual
    Property and Technology Licenses
        
    methods for template-based gene recombination to produce
    chimeric genes, including use of single or double-stranded
    templates; 10




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
    methods for recombining nucleic acid segments produced by
    incomplete nucleic acid chain extension reactions to produce
    chimeric genes, including the staggered extension process (StEP);
    methods utilizing reiterative screening or only a single cycle
    of screening;
    methods of combining any mutagenesis technique with DNA
    recombination methods to produce new chimeric genes;
    methods using synthesized nucleic acid fragments;
    in vivo and in vitro recombination methods of the above, in
    a variety of formats;
    methods of screening directed evolution libraries;
    methods for ligation- and single-stranded template-based
    recombination and reassembly;
    mutagenesis, including codon and gene site saturation
    mutagenesis, used in conjunction with recombination and
    reassembly;
    cell-based recombination methods; and
    fluorescence-, bioluminescence-, and nutrient-based screening
    methods, including the use of ultra-high throughput FACS-based
    methods for screening diverse variants.           11




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##### Table of Contents



Product
    Patents
    
    For our MAXY-G34 product candidates, we have three
    U.S. patents, 16 pending U.S. applications, six
    foreign patents and 30 pending foreign or international
    applications.
    For our MAXY-alpha product candidates, we have 20 pending
    U.S. applications and 47 pending foreign or international
    applications. Certain of these applications are jointly held by
    us and our collaborative partner, Roche.
    For our MAXY-VII product candidates, we have one
    U.S. patent, 21 pending U.S. applications, three
    foreign patents and 40 pending foreign or international
    applications. We also have exclusive licenses to two
    U.S. patents, ten pending U.S. applications and four
    pending foreign or international applications.
    For our MAXY-gamma product candidates, we have two
    U.S. patents, six pending U.S. applications, six
    foreign patents and 37 pending foreign or international
    applications.  Manufacturing
      Competition
      
    developing products;
    undertaking pre-clinical testing and clinical trials;
    obtaining FDA and other regulatory approvals of
    products; and
    manufacturing and marketing products.   12




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Research
    and Development Expenses
    Geographic
    Distribution
    Segment
    Reporting
    Government
    Regulation
       13




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
    Phase I:  Studies are conducted on normal,
    healthy human volunteers to determine safety, dosage tolerance,
    absorption, metabolism, distribution and excretion. If possible,
    Phase I studies may also be designed to gain early evidence
    of effectiveness.
    Phase II:  Studies are conducted on small
    groups of patients afflicted with a specific disease to
    determine dosage tolerance and optimal dosage, to gain
    preliminary evidence of efficacy, and to determine the common
    short-term side effects and risks associated with the substance
    being tested.
    Phase III:  Involves large-scale studies
    conducted on disease-afflicted patients to provide statistical
    evidence of efficacy and safety and to provide an adequate basis
    for physician labeling.          Environmental
    Regulation
    Employees
    Corporate
    Background and History
  (650) 298-5300.
   14




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Available
    Information
   PART IV  Item 15
    EXHIBITS,
    FINANCIAL STATEMENT SCHEDULES  15(a)(3)
    Exhibits.
  ExhibitNumber

Description of Exhibit2
.1

Exchange Agreement, dated as of
    April 12, 2000, by and among Maxygen, Inc., Maxygen
    Holdings Ltd., ProFound Pharma A/S and the shareholders of
    ProFound Pharma A/S(1)2
.2

Amendment No. 1 to the
    Exchange Agreement, dated as of July 31, 2000, by and among
    Maxygen, Inc., Maxygen Holdings Ltd., ProFound Pharma A/S and
    the shareholders of ProFound Pharma A/S(1)2
.3

Agreement and Plan of Merger,
    dated June 2, 2004, by and among Pioneer Hi-Bred
    International, Inc., Tango Merger Sub, Inc., Maxygen, Inc. and
    Verdia, Inc.(2)3
.1

Amended and Restated Certificate
    of Incorporation(3)3
.2

Amended and Restated Bylaws(3)4
.1

Specimen Common Stock Certificate
    (Exhibit 4.1 to Amendment No. 1)(4)*10
.1

Form of Executive Officer and
    Director Indemnification Agreement (Exhibit 10.7)(4)*10
.2

Form of Executive Officer Change
    of Control Plan (Exhibit 10.1)(5)*10
.3

Form of Amendment No. 1 to
    Executive Officer Change of Control Plan (Exhibit 10.3)(6)*10
.4

Form of Amendment No. 2 to
    Executive Officer Change of Control Plan (Exhibit 10.3)(7)*10
.5

1997 Stock Option Plan, as
    amended, with applicable option agreement(8)*10
.6

Form of Amendment to Stock Option
    Agreements (Exhibit 10.2)(7)*10
.7

1999 Nonemployee Directors Stock
    Option Plan, as amended, with applicable option agreement
    (Exhibit 10.3)(5)*10
.8

1999 Employee Stock Purchase Plan,
    as amended (Exhibit 10.11)(9)*10
.9

2000 International Stock Option
    Plan, as amended, with applicable option agreement (10)*10
.10

2000 Non-Officer Stock Option
    Plan, as amended, with applicable option agreement (11)*10
.11

2006 Equity Incentive Plan
    (including related form of stock option agreement)
    (Exhibit 10.4)(7)*10
.12

Form of Restricted Stock Unit
    Award Agreement under 2006 Equity Incentive Plan (12)10
.13

Lease, dated as of
    October 21, 1998, between Metropolitan Life Insurance
    Company and Maxygen, Inc. (Exhibit 10.4)(4) 15




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ExhibitNumber

Description of Exhibit10
.14

First Amendment to Lease, dated as
    of February 26, 1999, by and between Metropolitan Life
    Insurance Company and Maxygen, Inc. (Exhibit 10.5)(4)10
.15

Second Amendment to Lease, dated
    as of October 24, 2000, by and between Metropolitan Life
    Insurance Company and Maxygen, Inc. (Exhibit 10.6)(9)10
.16

Third Amendment to Lease, dated
    October 22, 2003, by and between Metropolitan Life
    Insurance Company and Maxygen, Inc. (Exhibit 10.15) (13)10
.17

Fourth Amendment to Lease dated
    December 15, 2004 by and between Metropolitan Life
    Insurance Company and Maxygen, Inc. (Exhibit 10.13) (14)10
.18

Fifth Amendment to Lease dated as
    of August 24, 2006, by and between Metropolitan Life
    Insurance Company and Maxygen, Inc. (Exhibit 10.2) (15)10
.19

Lease, dated December 15,
    2004, between Metropolitan Life Insurance Company and Maxygen,
    Inc. (Exhibit 10.14) (14)10
.20

First Amendment to Lease, dated as
    of August 24, 2006, by and between Metropolitan Life
    Insurance Company and Maxygen, Inc. (Exhibit 10.1) (15)10
.21

Lease Agreement, dated May 5,
    2000, between ProFound Pharma A/S and The Science Park in
    Horsholm (16)10
.22+

Technology Transfer Agreement,
    dated March 14, 1997 (effective March 1, 1998), among
    Maxygen, Inc., Affymax Technologies N.V. and Glaxo Group
    Limited, as amended (Exhibit 10.3 to Amendment
    No. 2)(4)*10
.23

Description of 2006 Executive
    Officer Cash Bonus Plan (Exhibit 10.1)(7)*10
.24

Description of Goldstein
    Reimbursement Arrangement (17)*10
.25#

Letter Agreement (re tax
    equalization payments), dated November 20, 2006, between
    Elliot Goldstein and Maxygen, Inc.10
.26+

Co-Development and
    Commercialization Agreement, dated as of December 9, 2005,
    among
    Hoffman-La Roche,
    Inc., F. Hoffman-La Roche Ltd. and Maxygen Holdings Ltd.
    (Exhibit 10.23) (18)10
.27#+

Cross License Agreement, dated as
    of July 16, 2003, between Maxygen, Inc. and Amgen Mountain
    View Inc. (as successor to Avidia, Inc.)10
.28+

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. (19)*10
.29

Consulting Agreement, dated as of
    January 12, 2006 (effective January 1, 2006), between
    Balkrishan Gill and Maxygen, Inc. (Exhibit 10.24) (18)*10
.30

Consulting Agreement, between the
    Company and Waverley Associates, Inc., dated as of April 1,
    2006 (20)21
.1#

List of Subsidiaries23
.1#

Consent of Independent Registered
    Public Accounting Firm24
.1#

Power of Attorney31
.1

Certification of Chief Executive
    Officer pursuant to Section 302 of the Sarbanes-Oxley Act
    of 200231
.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.#
    
    Previously filed with Maxygens Annual Report on Form
    10-K for the
    year ended December 31, 2006, as filed with the Commission
    on March 14, 2007.+
    
    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. 16




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(1)
    
    Incorporated by reference to the corresponding exhibit to
    Maxygens Current Report on
    Form 8-K
    (File
    No. 000-28401)
    filed with the Securities and Exchange Commission on
    August 15, 2000.(2)
    
    Incorporated by reference to Exhibit 2.1 to Maxygens
    Current Report on
    Form 8-K
    (File
    No. 000-28401)
    filed with the Securities and Exchange Commission on
    July 2, 2004.(3)
    
    Incorporated by reference to the corresponding exhibit to
    Maxygens Quarterly Report on
    Form 10-Q
    (File
    No. 000-28401)
    for the quarter ended June 30, 2000, filed with the
    Securities and Exchange Commission on August 14, 2000.(4)
    
    Incorporated by reference to the indicated exhibit to
    Maxygens Registration Statement on
    Form S-1,
    as amended
    (No. 333-89413)
    initially filed with the Securities and Exchange Commission on
    October 20, 1999.(5)
    
    Incorporated by reference to the indicated exhibit to
    Maxygens Quarterly Report on
    Form 10-Q
    (File
    No. 000-28401)
    for the quarter ended June 30, 2001, filed with the
    Securities and Exchange Commission on August 14, 2001.(6)
    
    Incorporated by reference to the indicated exhibit to
    Maxygens Annual Report on
    Form 10-K
    (File
    No. 000-28401)
    for the year ended December 31, 2002, filed with the
    Securities and Exchange Commission on March 27, 2003.(7)
    
    Incorporated by reference to the indicated exhibit to
    Maxygens Current Report on
    Form 8-K
    (File
    No. 000-28401)
    filed with the Securities and Exchange Commission on
    June 30, 2006).(8)
    
    Incorporated by reference to exhibit 10.1 to Maxygens
    Quarterly Report on
    Form 10-Q
    (File
    No. 000-28401)
    for the quarter ended June 30, 2002, filed with the
    Securities and Exchange Commission on August 14, 2002.(9)
    
    Incorporated by reference to the indicated exhibit to
    Maxygens Annual Report on
    Form 10-K
    (File
    No. 000-28401)
    for the year ended December 31, 2000, filed with the
    Securities and Exchange Commission on March 21, 2001.(10)
    
    Incorporated by reference to exhibit 10.6 to Maxygens
    Annual Report on
    Form 10-K
    (File
    No. 000-28401)
    for the year ended December 31, 2001, filed with the
    Securities and Exchange Commission on March 25, 2002.(11)
    
    Incorporated by reference to the exhibit 99.3 to
    Maxygens Registration Statement on
    Form S-8
    (No. 333-57486)
    filed with the Securities and Exchange Commission on
    March 23, 2001.(12)
    
    Incorporated by reference to the exhibit 4.2 to
    Maxygens Registration Statement on
    Form S-8
    (No. 333-138898)
    filed with the Securities and Exchange Commission on
    November 22, 2006.(13)
    
    Incorporated by reference to the indicated exhibit to
    Maxygens Annual Report on
    Form 10-K
    (File
    No. 000-28401)
    for the year ended December 31, 2003, filed with the
    Securities and Exchange Commission on March 12, 2004.(14)
    
    Incorporated by reference to the indicated exhibit to
    Maxygens Annual Report on
    Form 10-K
    (File
    No. 000-28401)
    for the year ended December 31, 2004, filed with the
    Securities and Exchange Commission on March 14, 2005.(15)
    
    Incorporated by reference to the indicated exhibit to
    Maxygens Current Report on
    Form 8-K
    (File
    No. 000-28401)
    filed with the Securities and Exchange Commission on
    August 25, 2006.(16)
    
    Incorporated by reference to exhibit 10.1 to Maxygens
    Quarterly Report on
    Form 10-Q
    (File
    No. 000-28401)
    for the quarter ended September 30, 2000, filed with the
    Securities and Exchange Commission on November 14, 2000.(17)
    
    Incorporated by reference to Exhibit 10.1 to Maxygens
    Current Report on
    Form 8-K
    (File
    No. 000-28401)
    filed with the Securities and Exchange Commission on
    February 7, 2005.(18)
    
    Incorporated by reference to the indicated exhibit to
    Maxygens Annual Report on
    Form 10-K
    (File
    No. 000-28401)
    for the year ended December 31, 2005, filed with the
    Securities and Exchange Commission on March 15, 2006.(19)
    
    Incorporated by reference to Exhibit 10.6 to Maxygens
    Quarterly Report on
    Form 10-Q
    (File
    No. 000-28401)
    for the quarter ended June 30, 2006, filed with the
    Securities and Exchange Commission on August 7, 2006.(20)
    
    Incorporated by reference to Exhibit 10.1 to Maxygens
    Current Report on
    Form 8-K
    (File
    No. 000-28401)
    filed with the Securities and Exchange Commission on
    April 4, 2006. 17




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SIGNATURES      By:
    /s/  Russell
    J. Howard       18




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EXHIBIT INDEX
  ExhibitNumber

Description of Exhibit2
.1

Exchange Agreement, dated as of
    April 12, 2000, by and among Maxygen, Inc., Maxygen
    Holdings Ltd., ProFound Pharma A/S and the shareholders of
    ProFound Pharma A/S(1)2
.2

Amendment No. 1 to the
    Exchange Agreement, dated as of July 31, 2000, by and among
    Maxygen, Inc., Maxygen Holdings Ltd., ProFound Pharma A/S and
    the shareholders of ProFound Pharma A/S (1)2
.3

Agreement and Plan of Merger,
    dated June 2, 2004, by and among Pioneer Hi-Bred
    International, Inc., Tango Merger Sub, Inc., Maxygen, Inc. and
    Verdia, Inc.(2)3
.1

Amended and Restated Certificate
    of Incorporation(3)3
.2

Amended and Restated Bylaws(3)4
.1

Specimen Common Stock Certificate
    (Exhibit 4.1 to Amendment No. 1) (4)*10
.1

Form of Executive Officer and
    Director Indemnification Agreement (Exhibit 10.7)(4)*10
.2

Form of Executive Officer Change
    of Control Plan (Exhibit 10.1)(5)*10
.3

Form of Amendment No. 1 to
    Executive Officer Change of Control Plan (Exhibit 10.3)(6)*10
.4

Form of Amendment No. 2 to
    Executive Officer Change of Control Plan (Exhibit 10.3)(7)*10
.5

1997 Stock Option Plan, as
    amended, with applicable option agreement(8)*10
.6

Form of Amendment to Stock Option
    Agreements (Exhibit 10.2)(7)*10
.7

1999 Nonemployee Directors Stock
    Option Plan, as amended, with applicable option agreement
    (Exhibit 10.3)(5)*10
.8

1999 Employee Stock Purchase Plan,
    as amended (Exhibit 10.11)(9)*10
.9

2000 International Stock Option
    Plan, as amended, with applicable option agreement(10)*10
.10

2000 Non-Officer Stock Option
    Plan, as amended, with applicable option agreement(11)*10
.11

2006 Equity Incentive Plan
    (including related form of stock option agreement)
    (Exhibit 10.4)(7)*10
.12

Form of Restricted Stock Unit
    Award Agreement under 2006 Equity Incentive Plan(12)10
.13

Lease, dated as of
    October 21, 1998, between Metropolitan Life Insurance
    Company and Maxygen, Inc. (Exhibit 10.4)(4)10
.14

First Amendment to Lease, dated as
    of February 26, 1999, by and between Metropolitan Life
    Insurance Company and Maxygen, Inc. (Exhibit 10.5)(4)10
.15

Second Amendment to Lease, dated
    as of October 24, 2000, by and between Metropolitan Life
    Insurance Company and Maxygen, Inc. (Exhibit 10.6)(9)10
.16

Third Amendment to Lease, dated
    October 22, 2003, by and between Metropolitan Life
    Insurance Company and Maxygen, Inc. (Exhibit 10.15)(13)10
.17

Fourth Amendment to Lease dated
    December 15, 2004 by and between Metropolitan Life
    Insurance Company and Maxygen, Inc. (Exhibit 10.13)(14)10
.18

Fifth Amendment to Lease dated as
    of August 24, 2006, by and between Metropolitan Life
    Insurance Company and Maxygen, Inc. (Exhibit 10.2)(15)10
.19

Lease, dated December 15,
    2004, between Metropolitan Life Insurance Company and Maxygen,
    Inc. (Exhibit 10.14)(14)10
.20

First Amendment to Lease, dated as
    of August 24, 2006, by and between Metropolitan Life
    Insurance Company and Maxygen, Inc. (Exhibit 10.1)(15)10
.21

Lease Agreement, dated May 5,
    2000, between ProFound Pharma A/S and The Science Park in
    Horsholm (16)10
.22+

Technology Transfer Agreement,
    dated March 14, 1997 (effective March 1, 1998), among
    Maxygen, Inc., Affymax Technologies N.V. and Glaxo Group
    Limited, as amended (Exhibit 10.3 to Amendment No.
    2) (4)*10
.23

Description of 2006 Executive
    Officer Cash Bonus Plan (Exhibit 10.1)(7)*10
.24

Description of Goldstein
    Reimbursement Arrangement(17) 19




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##### Table of Contents



ExhibitNumber

Description of Exhibit*10
.25#

Letter Agreement (re tax
    equalization payments), dated November 20, 2006, between
    Elliot Goldstein and Maxygen, Inc.10
.26+

Co-Development and
    Commercialization Agreement, dated as of December 9, 2005,
    among
    Hoffman-La Roche,
    Inc., F. Hoffman-La Roche Ltd. and Maxygen Holdings Ltd.
    (Exhibit 10.23)(18)10
.27#+

Cross License Agreement, dated as
    of July 16, 2003, between Maxygen, Inc. and Amgen Mountain
    View Inc. (as successor to Avidia, Inc.)10
.28+

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.(19)*10
.29

Consulting Agreement, dated as of
    January 12, 2006 (effective January 1, 2006), between
    Balkrishan Gill and Maxygen, Inc. (Exhibit 10.24)(18)*10
.30

Consulting Agreement, between the
    Company and Waverley Associates, Inc., dated as of April 1,
    2006 (20)21
.1#

List of Subsidiaries23
.1#

Consent of Independent Registered
    Public Accounting Firm24
.1#

Power of Attorney31
.1

Certification of Chief Executive
    Officer pursuant to Section 302 of the Sarbanes-Oxley Act
    of 200231
.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.#
    
    Previously filed with Maxygens Annual Report on Form
    10-K for the
    year ended December 31, 2006, as filed with the Commission
    on March 14, 2007.+
    
    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.(1)
    
    Incorporated by reference to the corresponding exhibit to
    Maxygens Current Report on
    Form 8-K
    (File
    No. 000-28401)
    filed with the Securities and Exchange Commission on
    August 15, 2000.(2)
    
    Incorporated by reference to Exhibit 2.1 to Maxygens
    Current Report on
    Form 8-K
    (File
    No. 000-28401)
    filed with the Securities and Exchange Commission on
    July 2, 2004.(3)
    
    Incorporated by reference to the corresponding exhibit to
    Maxygens Quarterly Report on
    Form 10-Q
    (File
    No. 000-28401)
    for the quarter ended June 30, 2000, filed with the
    Securities and Exchange Commission on August 14, 2000.(4)
    
    Incorporated by reference to the indicated exhibit to
    Maxygens Registration Statement on
    Form S-1,
    as amended
    (No. 333-89413)
    initially filed with the Securities and Exchange Commission on
    October 20, 1999.(5)
    
    Incorporated by reference to the indicated exhibit to
    Maxygens Quarterly Report on
    Form 10-Q
    (File
    No. 000-28401)
    for the quarter ended June 30, 2001, filed with the
    Securities and Exchange Commission on August 14, 2001.(6)
    
    Incorporated by reference to the indicated exhibit to
    Maxygens Annual Report on
    Form 10-K
    (File
    No. 000-28401)
    for the year ended December 31, 2002, filed with the
    Securities and Exchange Commission on March 27, 2003.(7)
    
    Incorporated by reference to the indicated exhibit to
    Maxygens Current Report on
    Form 8-K
    (File
    No. 000-28401)
    filed with the Securities and Exchange Commission on
    June 30, 2006).(8)
    
    Incorporated by reference to exhibit 10.1 to Maxygens
    Quarterly Report on
    Form 10-Q
    (File
    No. 000-28401)
    for the quarter ended June 30, 2002, filed with the
    Securities and Exchange Commission on August 14, 2002. 20




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##### Table of Contents



(9)
    
    Incorporated by reference to the indicated exhibit to
    Maxygens Annual Report on
    Form 10-K
    (File
    No. 000-28401)
    for the year ended December 31, 2000, filed with the
    Securities and Exchange Commission on March 21, 2001.(10)
    
    Incorporated by reference to exhibit 10.6 to Maxygens
    Annual Report on
    Form 10-K
    (File
    No. 000-28401)
    for the year ended December 31, 2001, filed with the
    Securities and Exchange Commission on March 25, 2002.(11)
    
    Incorporated by reference to the exhibit 99.3 to
    Maxygens Registration Statement on
    Form S-8
    (No. 333-57486)
    filed with the Securities and Exchange Commission on
    March 23, 2001.(12)
    
    Incorporated by reference to the exhibit 4.2 to
    Maxygens Registration Statement on
    Form S-8
    (No. 333-138898)
    filed with the Securities and Exchange Commission on
    November 22, 2006.(13)
    
    Incorporated by reference to the indicated exhibit to
    Maxygens Annual Report on
    Form 10-K
    (File
    No. 000-28401)
    for the year ended December 31, 2003, filed with the
    Securities and Exchange Commission on March 12, 2004.(14)
    
    Incorporated by reference to the indicated exhibit to
    Maxygens Annual Report on
    Form 10-K
    (File
    No. 000-28401)
    for the year ended December 31, 2004, filed with the
    Securities and Exchange Commission on March 14, 2005.(15)
    
    Incorporated by reference to the indicated exhibit to
    Maxygens Current Report on
    Form 8-K
    (File
    No. 000-28401)
    filed with the Securities and Exchange Commission on
    August 25, 2006.(16)
    
    Incorporated by reference to exhibit 10.1 to Maxygens
    Quarterly Report on
    Form 10-Q
    (File
    No. 000-28401)
    for the quarter ended September 30, 2000, filed with the
    Securities and Exchange Commission on November 14, 2000.(17)
    
    Incorporated by reference to Exhibit 10.1 to Maxygens
    Current Report on
    Form 8-K
    (File
    No. 000-28401)
    filed with the Securities and Exchange Commission on
    February 7, 2005.(18)
    
    Incorporated by reference to the indicated exhibit to
    Maxygens Annual Report on
    Form 10-K
    (File
    No. 000-28401)
    for the year ended December 31, 2005, filed with the
    Securities and Exchange Commission on March 15, 2006.(19)
    
    Incorporated by reference to Exhibit 10.6 to Maxygens
    Quarterly Report on
    Form 10-Q
    (File
    No. 000-28401)
    for the quarter ended June 30, 2006, filed with the
    Securities and Exchange Commission on August 7, 2006.(20)
    
    Incorporated by reference to Exhibit 10.1 to Maxygens
    Current Report on
    Form 8-K
    (File
    No. 000-28401)
    filed with the Securities and Exchange Commission on
    April 4, 2006. 21