<PAGE>

                                  UNITED STATES
                       SECURITIES AND EXCHANGE COMMISSION
                             Washington, D.C. 20549

                               -------------------

                                    FORM 10-Q



               QUARTERLY report pursuant to section 13 or 15(d) of
                       the Securities Exchange Act of 1934

                For the quarterly period ended September 30, 2001

                        Commission file number 000-28401

                                  MAXYGEN, INC.
             (Exact name of registrant as specified in its charter)

             Delaware                              77-0449487
     (State of incorporation)         (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)

                               -------------------

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 ____
                                     ---

As of November 1, 2001, there were 33,943,998 shares of the registrant's common
stock outstanding.

                                       1

<PAGE>

                                  MAXYGEN, INC.
                                    FORM 10-Q
                        QUARTER ENDED SEPTEMBER 30, 2001

<TABLE>
<CAPTION>
INDEX

Part I   FINANCIAL INFORMATION
<S>                                                                                                         <C>
Item 1:  Financial Statements:

         Condensed Consolidated Balance Sheets as of December 31, 2000
         and September 30, 2001 .........................................................................     3

         Condensed Consolidated Statements of Operations for the three and
         nine month periods ended September 30, 2000 and 2001 ...........................................     4

         Condensed Consolidated Statements of Cash Flows for the nine month
         periods ended September 30, 2000 and 2001 ......................................................     5

         Notes to Condensed Consolidated Financial Statements ...........................................     6

Item 2:  Management's Discussion and Analysis of Financial Condition and Results of Operations ..........    10

Item 3:  Quantitative and Qualitative Disclosures About Market Risk .....................................    24

Part II  OTHER INFORMATION

Item 1:  Legal Proceedings ..............................................................................    26

Item 2:  Changes in Securities and Use of Proceeds ......................................................    26

Item 3:  Defaults Upon Senior Securities ................................................................    26

Item 4:  Submission of Matters to a Vote of Security Holders ............................................    27

Item 5:  Other Information ..............................................................................    27

Item 6:  Exhibits and Reports on Form 8-K ...............................................................    27

SIGNATURES ..............................................................................................    28
</TABLE>

                                       2



<PAGE>

================================================================================
PART I - FINANCIAL INFORMATION
ITEM 1
FINANCIAL STATEMENTS

                                  MAXYGEN, INC.
                      CONDENSED CONSOLIDATED BALANCE SHEETS
                 (IN THOUSANDS, EXCEPT SHARE AND PER SHARE DATA)

<TABLE>
<CAPTION>
                                                                                   December 31,     September 30,
                                                                                       2000             2001
                                                                                   ------------     -------------
<S>                                                                                <C>              <C>
ASSETS                                                                               (Note 1)        (unaudited)
Current assets:
   Cash and cash equivalents ....................................................  $   111,374       $    56,684
   Short-term investments .......................................................      110,805           157,615
   Grant and other receivables ..................................................        8,425             9,058
   Prepaid expenses and other current assets ....................................        1,180             1,776
                                                                                   -----------       -----------
     Total current assets .......................................................      231,784           225,133
   Property and equipment, net ..................................................        9,916            14,320
   Goodwill and other intangible assets, net of accumulated amortization of
     $3,418 at December 31, 2000 and $9,963 at September 30, 2001 ...............       22,760            16,216
   Long-term investments ........................................................       35,836            30,484
   Deposits and other assets ....................................................        1,403             1,601
                                                                                   -----------       -----------
     Total assets ...............................................................  $   301,699       $   287,754
                                                                                   ===========       ===========

LIABILITIES AND STOCKHOLDERS' EQUITY
Current liabilities:
   Accounts payable .............................................................  $     2,143       $     3,456
   Accrued compensation .........................................................        1,859             4,261
   Other accrued liabilities ....................................................        4,633             4,004
   Deferred revenue .............................................................        6,228             8,739
   Current portion of equipment financing obligations ...........................          533               604
                                                                                   -----------       -----------
     Total current liabilities ..................................................       15,396            21,064
Deferred revenue ................................................................        2,810             3,588
Non-current portion of equipment financing obligations ..........................        1,295               835
Commitments
Stockholders' equity:
   Preferred stock, $0.0001 par value, 5,000,000 shares authorized, no
     shares issued and outstanding at December 31, 2000 and September 30,
     2001 .......................................................................           --                --

   Common stock, $0.0001 par value: 100,000,000 shares authorized,
     33,576,736, and 33,939,998 shares issued and outstanding at
     December 31, 2000 and September 30, 2001, respectively .....................            3                 3
   Additional paid-in capital ...................................................      386,026           388,587
   Notes receivable from stockholders ...........................................         (776)             (749)
   Deferred stock compensation ..................................................      (19,880)          (10,469)
   Accumulated other comprehensive income .......................................          587             2,153
   Accumulated deficit ..........................................................      (83,762)         (117,258)
                                                                                   -----------       -----------
     Total stockholders' equity .................................................      282,198           262,267
                                                                                   -----------       -----------
     Total liabilities and stockholders' equity .................................  $   301,699       $   287,754
                                                                                   ===========       ===========
</TABLE>

                             See accompanying notes.

                                       3

<PAGE>

                                  MAXYGEN, INC.
                 CONDENSED CONSOLIDATED STATEMENTS OF OPERATIONS
                 (IN THOUSANDS, EXCEPT SHARE AND PER SHARE DATA)
                                   (UNAUDITED)

<TABLE>
<CAPTION>
                                                                              Three Months Ended              Nine Months Ended
                                                                                 September 30,                    September 30,
                                                                         ---------------------------    --------------------------
                                                                             2000             2001           2000           2001
                                                                         -----------     -----------    -----------    -----------
<S>                                                                      <C>             <C>            <C>            <C>
Collaborative research and development revenue ......................    $     3,178     $     6,384    $     9,419    $    17,381
Grant revenue .......................................................          2,784           1,026          8,112          4,635
                                                                         -----------     -----------    -----------    -----------
Total revenues ......................................................          5,962           7,410         17,531         22,016
Operating expenses:
    Research and development ........................................         11,582          13,468         25,656         39,195
    General and administrative ......................................          2,881           3,168          7,736         10,668
    Stock compensation expense (1) ..................................          2,767           2,674         10,870          9,729
    Acquired in-process research and development ....................         28,047               -         28,959              -
    Amortization of goodwill and other intangible assets ............          1,847           2,182          1,847          6,545
                                                                         -----------     -----------    -----------    -----------
Total operating expenses ............................................         47,124          21,492         75,068         66,137
                                                                         -----------     -----------    -----------    -----------
Loss from operations ................................................        (41,162)        (14,082)       (57,537)       (44,121)
Interest income, net ................................................          4,415           3,196         10,806         10,625
                                                                         -----------     -----------    -----------    -----------
Net loss ............................................................    $   (36,747)    $   (10,886)   $   (46,731)   $   (33,496)
                                                                         ===========     ===========    ===========    ===========
Basic and diluted net loss per share ................................    $     (1.18)    $     (0.33)   $     (1.57)   $     (1.03)
Shares used in computing basic and diluted net loss per
    share ...........................................................     31,165,347      32,707,236     29,805,258     32,475,108

----------
(1)   Stock compensation expense related to the following:
      Research and development ......................................    $     1,652     $     2,080    $     7,080    $     7,831
      General and administrative ....................................          1,115             594          3,790          1,898
                                                                         -----------     -----------    -----------    -----------
                                                                         $     2,767     $     2,674    $    10,870    $     9,729
                                                                         ===========     ===========    ===========    ===========
</TABLE>

                             See accompanying notes.

                                       4

<PAGE>

                                  MAXYGEN, INC.
                 CONDENSED CONSOLIDATED STATEMENTS OF CASH FLOWS
                 (IN THOUSANDS, EXCEPT SHARE AND PER SHARE DATA)
                                   (UNAUDITED)

<TABLE>
<CAPTION>
                                                                                      Nine Months Ended
                                                                                        September 30,
                                                                                ----------------------------
                                                                                     2000           2001
                                                                                ------------    ------------
<S>                                                                             <C>             <C>
Operating activities
Net loss ....................................................................   $    (46,731)   $   (33,496)
Adjustments to reconcile net loss to net cash used in operating activities:
    Depreciation and amortization ...........................................          1,020          2,150
    Amortization of intangible assets .......................................          1,848          6,545
    Deferred stock compensation amortization ................................          8,107          9,411
    Common stock issued and stock options granted to
        consultants for services rendered ...................................          2,763            772
    Common stock issued for technology ......................................            958             --
    Acquired in-process research and development ............................         28,959             --
    Changes in operating assets and liabilities:
        Grant and other receivables .........................................         (4,942)          (633)
        Prepaid expenses and other current assets ...........................           (296)          (596)
        Deposits and other assets ...........................................           (264)          (198)
        Accounts payable ....................................................         (4,402)         1,313
        Accrued compensation ................................................          2,552          2,402
        Other accrued liabilities ...........................................          1,867           (629)
        Deferred revenue ....................................................          1,216          3,289
        Other ...............................................................            (90)            --
                                                                                ------------    -----------
Net cash used in operating activities .......................................         (7,435)        (9,670)
                                                                                ------------    -----------
Investing activities
Cash acquired in acquisitions ...............................................            349             --
Purchases of available-for-sale securities ..................................        (92,521)      (161,306)
Sale of available-for-sale securities .......................................             --         15,237
Maturities of available-for-sale securities .................................         10,000        106,292
Acquisition of property and equipment .......................................         (2,503)        (6,554)
                                                                                ------------    -----------
Net cash used in investing activities .......................................        (84,675)       (46,331)
                                                                                ------------    -----------
Financing activities
Borrowings under equipment financing obligation .............................            166             --
Repayments under equipment financing obligation .............................            (76)          (389)
Equity adjustment from foreign currency translation .........................             --           (115)
Proceeds from issuance of common stock - net of issuance costs ..............        138,204          1,788
Payments received on promissory notes .......................................            604             27
                                                                                ------------    -----------
Net cash provided by financing activities ...................................        138,898          1,311
                                                                                ------------    -----------
Net increase (decrease) in cash and cash equivalents ........................         46,788        (54,690)
Cash and cash equivalents at beginning of period ............................        136,343        111,374
                                                                                ------------    -----------
Cash and cash equivalents at end of period ..................................   $    183,131    $    56,684
                                                                                ============    ===========
Schedule of non-cash financing activities
Tangible and intangible assets acquired in acquisition transaction for
   shares of common stock, net of cash acquired and liabilities assumed .....   $     37,399    $        --
Shares issued to acquire technology .........................................   $        958    $        --
</TABLE>

                             See accompanying notes.

                                       5

<PAGE>

                                  MAXYGEN, INC.

              NOTES TO CONDENSED CONSOLIDATED FINANCIAL STATEMENTS
                                   (unaudited)

1.  Basis of Presentation and Significant Accounting Policies

Basis of Presentation

The accompanying unaudited consolidated financial statements have been prepared
in accordance with generally accepted accounting principles for interim
financial information. The information as of September 30, 2001 and for the
three months and nine months ended September 30, 2000 and September 30, 2001
includes all adjustments (consisting only of normal recurring adjustments) that
the management of the Company believes necessary for fair presentation of the
results for the periods presented.

Results for any interim period are not necessarily indicative of results for any
future interim period or for the entire year. The accompanying consolidated
financial statements should be read in conjunction with the financial statements
and notes thereto included in the Company's Report on Form 10-K for the year
ended December 31, 2000.

Principles of Consolidation

The condensed consolidated financial statements include the accounts of the
Company and its subsidiaries. All significant intercompany balances and
transactions have been eliminated in consolidation.

Revenue Recognition

Non-refundable up-front payments received in connection with research and
development collaboration agreements, including technology advancement funding
that is intended for the development of the Company's core technology, are
deferred and recognized on a straight-line basis over the relevant periods
specified in the agreement, generally the research term.

Revenue related to collaborative research with the Company's corporate
collaborators is recognized as research services are performed over the related
funding periods for each contract. Under these agreements, the Company is
required to perform research and development activities as specified in each
respective agreement. The payments received under each respective agreement are
not refundable and are generally based on a contractual cost per full-time
equivalent employee working on the project. Research and development expenses
under the collaborative research agreements approximate or exceed the revenue
recognized under such agreements over the term of the respective agreements.
Deferred revenue may result when the Company does not incur the required level
of effort during a specific period in comparison to funds received under the
respective contracts. Payments received related to substantive, at-risk
incentive milestones, if any, are recognized as revenue upon achievement of the
incentive milestone event because the Company has no future performance
obligations related to the payment. Incentive milestone payments are triggered
either by the results of the Company's research efforts or by events external to
the Company, such as regulatory approval to market a product. Royalties, if any,
are recognized when earned.

The Company has also been awarded grants from the Defense Advanced Research
Projects Agency ("DARPA"), National Institute of Standards and
Technology-Advanced Technology Program ("NIST-ATP") and the U.S. Agency for
International Development ("USAID") for various research and development
projects. The terms of these grant agreements are three years with various
termination dates, the last of which is September 2004 for the existing
agreements. Revenue related to grant agreements is recognized as related
research and development expenses are incurred.

                                       6

<PAGE>

Net loss per share

Basic and diluted net loss per common share are presented in conformity with the
Statement of Financial Accounting Standards No. 128, "Earnings per Share" ("SFAS
128"), for all periods presented. In accordance with SFAS 128, basic and diluted
net loss per share has been computed using the weighted-average number of shares
of common stock outstanding during the period, less shares subject to
repurchase.

The following table presents the calculation of basic and diluted net loss per
share (in thousands, except share and per share data):

<TABLE>
<CAPTION>
                                                                 Three Months Ended              Nine Months Ended
                                                                   September 30,                   September 30,
                                                            -----------------------------   ----------------------------
                                                                2000             2001           2000             2001
                                                            ------------     ------------   ------------     -----------
<S>                                                         <C>              <C>            <C>              <C>
Net loss ...............................................    $    (36,747)    $    (10,886)  $    (46,731)    $   (33,496)
                                                            ============     ============   ============     ===========
Basic and diluted:
   Weighted-average shares of common stock
     outstanding .......................................      33,001,899       33,853,501     32,097,930      33,781,016
   Less: weighted-average shares subject to
     repurchase ........................................      (1,836,552)      (1,146,265)    (2,292,672)     (1,305,908)
                                                            ------------     ------------   ------------     -----------
   Weighted-average shares used in computing
     basic and diluted net loss per share ..............      31,165,347       32,707,236     29,805,258      32,475,108
                                                            ============     ============   ============     ===========
Basic and diluted net loss per share ...................    $      (1.18)    $      (0.33)  $      (1.57)    $     (1.03)
                                                            ============     ============   ============     ===========
</TABLE>


The Company has excluded all outstanding stock options and shares subject to
repurchase from the calculation of diluted loss per common share because all
such securities are antidilutive for all applicable periods presented. The total
number of shares excluded from the calculations of diluted net loss per share,
prior to application of the treasury stock method for options, was 5,715,000 at
September 30, 2000 and 8,322,595 at September 30, 2001. Such securities, had
they been dilutive, would have been included in the computations of diluted net
loss per share along with restricted common stock subject to the Company's right
of repurchase.

Comprehensive Income (Loss)

Comprehensive income (loss) is primarily comprised of net unrealized gains or
losses on available-for-sale securities and foreign currency translation
adjustments. Comprehensive income (loss) and its components for the three and
nine month periods ended September 30, 2000 and 2001 are as follows (in
thousands):

<TABLE>
<CAPTION>
                                                                 Three Months Ended              Nine Months Ended
                                                                   September 30,                   September 30,
                                                            -----------------------------   ----------------------------
                                                                2000             2001           2000             2001
                                                            ------------     ------------   ------------     -----------
<S>                                                         <C>              <C>            <C>              <C>
Net loss ...............................................    $    (36,747)    $    (10,886)  $    (46,731)    $   (33,496)
Changes in unrealized gain on securities
   available-for-sale ..................................             147              900             17           1,681
Changes in foreign currency translation
   adjustments .........................................             (90)           1,118            (90)           (115)
                                                            ------------     ------------   ------------     -----------
Comprehensive loss .....................................    $    (36,690)    $     (8,868)  $    (46,804)    $   (31,930)
                                                            ============     ============   ============     ===========
</TABLE>

The components of accumulated other comprehensive income(loss) are as follows
(in thousands):

<TABLE>
<CAPTION>
                                                               December 31,  September 30,
                                                                  2000          2001
                                                               ------------  -------------
<S>                                                            <C>           <C>
Unrealized gains on securities available-for-sale .........      $    521      $    2,202
Foreign currency translation adjustments ..................            66             (49)
                                                                 --------      ----------
Accumulated other comprehensive income ....................      $    587      $    2,153
                                                                 ========      ==========
</TABLE>

                                       7

<PAGE>

Derivatives and Financial Instruments

Effective October 1, 2000, the Company adopted Statement of Financial Accounting
Standards ("SFAS") No. 133, "Accounting for Derivative Instruments and Hedging
Activities" ("SFAS 133"), which establishes accounting and reporting standards
for derivative instruments, including certain derivative instruments embedded in
other contracts (collectively referred to as derivatives), and for hedging
activities. SFAS 133 was later amended by SFAS No. 137 and SFAS No. 138. This
standard requires that an entity recognize all derivatives as either assets or
liabilities in the statement of financial position and measure those instruments
at fair value. The adoption of this standard did not have a material effect on
the Company's consolidated financial position, results of operations or cash
flows. At September 30, 2001, the Company had foreign currency contracts in the
form of forward exchange contracts totaling $5.3 million.

2.  Investments

Management determines the appropriate classification of debt securities at the
time of purchase and reevaluates such designation as of each balance sheet date.
The Company's debt securities are classified as available-for-sale and are
carried at estimated fair value in cash equivalents and short-term investments.
Unrealized gains and losses are reported as accumulated other comprehensive
income (loss) in stockholders' equity. The amortized cost of debt securities in
this category is adjusted for amortization of premiums and accretion of
discounts to maturity. Such amortization is included in interest income.
Realized gains and losses on available-for-sale securities are included in
interest income and expense. The cost of securities sold is based on the
specific identification method. Interest and dividends on securities classified
as available-for-sale are included in interest income. The Company's cash
equivalents and investments as of September 30, 2001 are as follows (in
thousands):

<TABLE>
<CAPTION>
                                                                              Gross         Gross
                                                             Amortized     Unrealized     Unrealized     Estimated
                                                               Cost           Gains         Losses       Fair Value
                                                           ------------   ------------   ------------   ------------
<S>                                                        <C>            <C>            <C>            <C>
Money market funds ......................................  $     56,684   $         --   $         --   $     56,684
Commercial paper ........................................       155,966          1,649             --        157,615
Corporate bonds .........................................        29,931            553             --         30,484
                                                           ------------   ------------   ------------   ------------
   Total ................................................       242,581          2,202             --        244,783
Less amounts classified as cash equivalents .............       (56,684)            --             --        (56,684)
                                                           ------------   ------------   ------------   ------------
Total investments .......................................  $    185,897   $      2,202   $         --   $    188,099
                                                           ============   ============   ============   ============
</TABLE>


There was $173,000 in realized gains or losses on the sale of available-for-sale
securities for both the three and nine month periods ended September 30, 2001.
There were no realized gains or losses on the sale of available-for-sale
securities in the comparable periods of 2000.

At September 30, 2001, the contractual maturities of investments were as follows
(in thousands):

<TABLE>
<CAPTION>
                                                   Amortized      Estimated
                                                      Cost       Fair Value
                                                   ---------      ---------
<S>                                                <C>            <C>
       Due within one year ......................  $ 212,650      $ 214,299
       Due after one year .......................     29,931         30,484
                                                   ---------      ---------
                                                   $ 242,581      $ 244,783
                                                   =========      =========
</TABLE>


3.  Collaborative Agreements

ALK-Abello A/S

In February 2001, the Company established a three-year collaboration with
ALK-Abello A/S, a wholly owned subsidiary of Chr. Hansen Holding A/S, Denmark,
to research and develop novel recombinant therapeutics for the treatment of
specific allergies. The Company will collaborate with ALK-Abello to create
therapies for treating specific allergies, including allergies to house dust
mites and grass, which are the cause of many common allergies. Under the terms
of the collaboration, the Company will receive license fees, technology access
fees, research and development funding, and potential milestone

                                       8

<PAGE>

payments. Such payments to the Company, including milestone payments, could
total a maximum of $80 million. The Company will also be entitled to receive
royalties on product sales, if any. ALK-Abello will receive exclusive worldwide
rights to commercialize all recombinant human therapeutics developed in the
collaboration.

International AIDS Vaccine Initiative

In February 2001, the Company established a three-year collaboration with the
International AIDS Vaccine Initiative and DBLV, LLC, an entity established and
funded by the Rockefeller Foundation to develop novel HIV vaccines. Under the
agreement, DBLV will provide full research and development funding to the
Company for at least three years to expand the Company's ongoing program in HIV
vaccine development. The Company will retain all rights to commercialize the HIV
vaccine candidates in all developed countries of the world, as well as in
certain markets in the developing world.

InterMune, Inc.

In September 2001, Maxygen Holdings Ltd., a wholly owned subsidiary of the
Company, entered into a license and collaboration agreement with InterMune, Inc.
("InterMune") to develop and commercialize novel, next-generation interferon
gamma products. Under the terms of the agreement, InterMune will take product
candidates developed by the Company into clinical development. InterMune will
fund optimization and development of the next-generation interferon gamma
products, and will retain exclusive worldwide commercialization rights for all
human therapeutic indications. Under the terms of the collaboration agreement,
the Company will receive up-front license fees, research and development
funding, and potential development and commercialization milestone payments.
Such payments to the Company, including milestone payments, could exceed $60
million. In addition, the Company will also be entitled to receive royalties on
product sales, if any.

4.  Government Grant

USAID Cooperative Grant

In September 2001, the Company was awarded a $3.7 million, three-year grant from
the U.S. Agency for International Development ("USAID") to support the research
and development of a novel, broadly protective malaria vaccine. Under the terms
of the grant, Maxygen will retain worldwide rights to commercialize successful
vaccine candidates that may result from the research and development.

5.  New Accounting Pronouncements

In June 2001, the Financing Accounting Standards Board issued Statements of
Financial Accounting Standards No. 141, Business Combinations, and No. 142,
Goodwill and Other Intangible Assets, effective for fiscal years beginning after
December 15, 2001. Under the new rules, goodwill will no longer be amortized but
will be subject to annual impairment tests in accordance with Statement No. 142.
Other intangible assets will continue to be amortized over the useful lives.

The Company will apply the new rules on accounting for goodwill and other
intangible assets beginning in the first quarter of 2002. Application of the
nonamortization provisions of the Statement is expected to result in a decrease
in net loss of $8.7 million in 2002 and $5.3 million in 2003. During 2002, the
Company will perform the first of the required impairment tests of goodwill and
indefinite lived intangible assets as of January 1, 2002 and has not yet
determined what the effect of these tests will be on the earnings and financial
position of the Company.

                                       9

<PAGE>

================================================================================

Forward Looking Statements

This report contains forward-looking statements within the meaning of federal
securities laws that relate to future events or our future financial
performance. In some cases, you can identify forward-looking statements by
terminology such as "may," "can," "will," "should," "expect," "plan,"
"anticipate," "believe," "estimate," "predict," "intend," "potential" or
"continue" or the negative of these terms or other comparable terminology. Risks
and uncertainties and the occurrence of other events could cause actual results
to differ materially from these predictions. Factors that could cause or
contribute to such differences include those discussed below under "--Risk
Factors That May Affect Results of Operations and Financial Condition," as well
as those discussed in our Annual Report on Form 10-K for the year ended December
31, 2000.

Although we believe that the expectations reflected in the forward-looking
statements are reasonable, we cannot guarantee future results, levels of
activity, performance or achievements. Moreover, neither we nor any other person
assumes responsibility for the accuracy and completeness of these statements. We
are under no duty to update any of the forward-looking statements after the date
of this report or to conform these statements to actual results.

================================================================================

ITEM 2
MANAGEMENT'S DISCUSSION AND ANALYSIS OF FINANCIAL CONDITION AND RESULTS OF
OPERATIONS

Overview

Maxygen was founded in May 1996 and began operations in March 1997. To date, we
have generated revenues from research collaborations with agriculture,
pharmaceutical, petroleum, and chemical companies and from government grants.
Our current collaborators are Novozymes, DuPont, Pfizer, Syngenta, DSM, Rio
Tinto, Lundbeck, Chevron, Hercules, ALK-Abello, IAVI, InterMune and Aventis
Pasteur SA. Our government grants are from the Defense Advanced Research
Projects Agency, the National Institute of Standards and Technology-Advanced
Technology Program and the U.S. Agency for International Development.

Revenue under strategic alliances and government grants increased from $14.0
million in 1999 to $24.5 million in 2000 and was $22.0 million in the nine
months ended September 30, 2001. Revenues may fluctuate from period to period
and there can be no assurance that these collaboration agreements will continue
for their initial term or beyond.

We have incurred significant losses since our inception. As of September 30,
2001, our accumulated deficit was $117.3 million and total stockholders' equity
was $262.3 million. We have invested heavily in establishing our proprietary
technologies. These investments have contributed to the increases in operating
expenses from $26.7 million in 1999 to $99.4 million in 2000 and $66.1 million
in the nine months ended September 30, 2001. Our total headcount increased from
143 employees at the end of 1999 to 252 employees at the end of 2000. As of
September 30, 2001 Maxygen had 297 employees, of whom 84% were engaged in
research and development. We expect to incur additional operating losses over at
least the next several years as we continue to expand our research and
development efforts and infrastructure.

Source of Revenue and Revenue Recognition Policy

We recognize revenues from research collaboration agreements as earned upon
achievement of the performance requirements of the agreements. Revenue related
to grant agreements is recognized as related research and development expenses
are incurred. Our existing corporate collaboration agreements generally provide
for research funding for a specified number of full time researchers working in
defined research programs. Revenue related to these payments is earned as the
related research work

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is performed. In addition, these collaborators generally make technology
advancement payments that are intended to fund development of our core
technology, as opposed to a defined research program. These payments are
recognized ratably over the applicable funding period. Payments received that
are related to future performance are deferred and recognized as revenue as the
performance requirements are achieved. As of September 30, 2001, we have
deferred revenues of approximately $12.3 million. Our sources of potential
revenue for the next several years are likely to be license, research,
technology advancement and milestone payments under existing and possible future
collaborative arrangements, government research grants, and royalties from our
collaborators based upon revenues received from any products commercialized
under those agreements.

Deferred Compensation

Deferred compensation for options granted to employees has been determined as
the difference between the deemed fair market value for financial reporting
purposes of our common stock on the date the applicable options were granted and
the exercise price. Deferred compensation for options granted to consultants has
been determined in accordance with Statement of Financial Accounting Standards
No. 123 as the fair value of the equity instruments issued. Compensation for
related options granted to consultants is periodically remeasured as the
underlying options vest.

In connection with the grant of stock options to employees before our initial
public offering, we recorded deferred stock compensation of approximately $2.4
million in 1998 and $19.5 million in 1999. These amounts were initially recorded
as a component of stockholders' equity and are being amortized as charges to
operations over the vesting period of the options using a graded vesting method.
We recognized stock compensation expense of approximately $4.9 million in 1999,
$7.8 million in 2000 and $3.7 million in the nine months ended September 30,
2001 related to the deferred compensation amortization on these option grants.
In connection with the grant of stock options to consultants, we recorded stock
compensation expense of $800,000 in 1999, $3.0 million in 2000 and $211,000 in
the nine months ended September 30, 2001. Due to the acceleration of an
executive stock option award, an additional $1.6 million stock compensation
expense was recorded in 2000.

In connection with the Maxygen ApS acquisition in August 2000, stock options
were granted in exchange for outstanding warrants to purchase Maxygen ApS
securities. In connection with this exchange we recorded aggregate deferred
compensation totaling $1.5 million. This amount is being amortized over the
remaining vesting period of the options, of which $298,000 was expensed in 2000
and $536,000 in the nine months ended September 30, 2001. For the shares
exchanged that had a right of repurchase, deferred compensation of $13.1 million
was recorded. This amount is being amortized to expense over a three year graded
vesting period. A total of $3.3 million was recognized as expense in 2000 and
$5.3 million in the nine months ended September 30, 2001.

Results of Operations

         Revenues

Our total revenues increased from $6.0 million and $17.5 million in the three
and nine months ended September 30, 2000, to $7.4 million and $22.0 million in
the comparable periods of 2001. The increase in collaborative research and
development revenue was due to additional strategic alliances and the expansion
of existing alliances. The decline in grant revenue reflects the expiration of
three government grants that began in late 1997, early 1998 and early 1999. We
expect our total revenues to increase in the remainder of 2001 as new projects
are initiated under existing collaboration agreements and as new collaboration
arrangements are consummated.

         Research and Development Expenses

Our research and development expenses consist primarily of salaries and other
personnel-related expenses, facility costs, supplies and depreciation of
facilities and laboratory equipment. Research and development expenses increased
from $13.2 million and $32.7 million in the three and nine months ended
September 30, 2000, to $15.5 million and $47.0 million in the comparable periods
of 2001. Also included in research and development expenses is stock
compensation expense of $1.7 million and $7.1 million in the three and nine
months ended September 30, 2000 and $2.1 million and $7.8 million in the
comparable periods of 2001. The increase is primarily due to our accelerated
efforts in all aspects of research and

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development, including increased expenditures resulting from our acquisition of
Maxygen ApS in August 2000, as well as investments in our technology platforms
and in the development of product candidates.

Research and development expenses represented 222% and 187% of total revenues in
the three and nine months ended September 30, 2000 and 210% and 214% of total
revenues in the comparable periods of 2001. The decrease between quarters is
primarily due to growth in our total revenue between periods. The increase
between the nine months ended September 30, 2000 and 2001 was due primarily to
increased staff necessary to manage and support our growth plus increased
research and development costs resulting from our acquisition of Maxygen ApS,
offset in part by the growth in our total revenues.

We expect research and development cost to increase during the remainder of 2001
as new projects are initiated under existing collaboration agreements and as new
collaboration arrangements are consummated. We expect to continue to devote
substantial resources to research and development, and we expect that research
and development expenses will continue to increase in absolute dollars for at
least the next several years. The acquisition of Maxygen ApS has significantly
increased our research and development expenses in absolute dollars.

         General and Administrative Expenses

Our general and administrative expenses consist primarily of personnel costs for
finance, human resources, business development, legal and general management, as
well as professional expenses, such as legal and accounting. General and
administrative expenses decreased from $4.0 million in the three months ended
September 30, 2000 to $3.8 million in the comparable quarter for 2001. Expenses
increased from $11.5 million in the nine months ended September 30, 2000 to
$12.6 million in the comparable period for 2001. Also included in general and
administrative expenses is stock compensation expense of $1.1 million and $3.8
million in the three and nine months ended September 30, 2000, and $594,000 and
$1.9 million in the comparable periods of 2001. The decrease in total general
and administrative expenses between comparable quarters is primarily due to
lower stock compensation expense. Expenses increased between the nine months
ended September 30, 2000 and 2001 primarily due to increased staffing necessary
to manage and support our growth offset by lower stock compensation expense.

General and administrative expenses represented 67% and 66% of total revenues
for the three and nine months ended September 30, 2000, and 51% and 57% of total
revenues for the comparable periods of 2001. The decrease was due primarily to
the growth in our total revenue between periods.

We expect that our general and administrative expenses will increase in absolute
dollar amounts for at least the next several years as we expand our legal and
accounting staff, add infrastructure and investor relations programs and
increased professional fees and insurance premiums. We expect that general and
administrative expenses as a percentage of total revenue will continue to
decrease as our revenues increase and research and development activities expand
more quickly than our general and administrative expenses.

            In-Process Research and Development

On May 8, 2000, we acquired certain in-process technology through the
acquisition of a privately held California corporation. In connection with the
acquisition we issued 39,600 shares of our common stock. Pursuant to the terms
of the acquisition agreement, 18,500 shares of our common stock are being held
in escrow until such time contingencies regarding the patents related to the
acquired technology are resolved. Accordingly, we have recorded a charge for
acquired in-process research and development of $912,000 representing the fair
value of the 21,100 shares delivered to the sellers at closing, plus certain
transaction expenses. Shares in escrow will be valued and accounted for when,
and if, the contingencies are resolved and the shares are delivered to the
sellers. As opportunities present themselves, we intend to continue to acquire
new technologies and companies. Such acquisitions could lead to additional
direct and indirect expenses that could negatively affect our results of
operations.

On August 10, 2000, we acquired Maxygen ApS for total consideration of
approximately $71.8 million, including $5.5 million for the assumption of
liabilities and $1.0 million for estimated acquisition costs. Prior to the
acquisition, Maxygen ApS was a Danish privately-held, development-stage company
that had minimal revenues since its inception in April 1999. Maxygen ApS is
focused on the development of improved second-generation protein pharmaceutical
products and has developed broad pre-clinical

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<PAGE>

development capabilities and proprietary technologies and expertise that help to
address traditional shortcomings of protein pharmaceuticals such as half-life,
stability and immunogenicity. Approximately $28.0 million of the total purchase
price represented the value of in-process research and development projects that
are at a pre-clinical stage of development, had not yet reached technological
feasibility, and had no alternative future use. This amount was charged to our
operations in the third quarter ended September 30, 2000. The acquisition was
accounted for under the purchase method of accounting. Accordingly, the results
of operations of Maxygen ApS are included in the condensed consolidated
financial statements from August 10, 2000.

The $28.0 million in-process research and development charge represents the
value determined by an independent appraiser, using a discounted cash flow
methodology, to be attributable to the six pre-clinical stage in-process
research and development projects of Maxygen ApS based on a valuation analysis
of such research and development. In-process technology was expensed upon
acquisition as technological feasibility had not been established and no
alternative future uses existed. To value the in-process technology we
considered, among other factors, the stage of development of each project, the
time and resources needed to complete each project, expected income and
associated risks. Associated risks included the inherent difficulties and
uncertainties in completing the project, in obtaining regulatory approval to
market, and the risks related to the viability of and potential changes to
future target markets. The charge relates to specific on-going research and
development. Management of Maxygen believes that the allocation of the purchase
price to in-process research and development was appropriate given the future
potential of this research and development to contribute to the operations of
Maxygen. Assuming this research continues through all stages of clinical
development, we project substantial future research and development expenditures
related to this technology.

We continue to fund and develop the certain-of in-process research and
development projects acquired through Maxygen ApS. There can be no assurances
that the in-process projects acquired will achieve technological feasibility or
that we will be able to successfully market products based on such technology.

            Goodwill and Other Intangible Assets

In connection with the Maxygen ApS acquisition, we allocated $26.2 million to
goodwill and other intangible assets and will amortize this goodwill and other
intangible assets over three years, the term of expected benefit. We believe
this term is reasonable given that Maxygen ApS was a development stage entity
and its technology was at an early stage of development and was yet unproven.
Amortization expense of $3.4 million in 2000 and $6.5 million in the nine months
ended September 30, 2001 was recorded on goodwill and other intangible assets.

Goodwill and other intangible assets are generally evaluated on an individual
acquisition or market basis whenever events or changes in circumstances indicate
that such assets are impaired or the estimated useful lives are no longer
appropriate. If indicators of impairment exist, we will review our long-lived
assets (including goodwill) for impairment based on estimated future discounted
cash flows attributable to the assets. In the event such cash flows are not
expected to be sufficient to recover the recorded value of the assets, the
assets are written down to their estimated fair values. No impairment charges
have been recorded in 2000 or in the nine months ended September 30, 2001.

In June 2001, the Financial Accounting Standards Board issued Statements of
Financial Accounting Standards No. 141, Business Combinations, and No. 142,
Goodwill and Other Intangible Assets, effective for fiscal years beginning after
December 15, 2001. Under the new rules, goodwill will no longer be amortized but
will be subject to annual impairment tests in accordance with Statement No. 142.
Other intangible assets will continue to be amortized over the useful lives.

We will apply the new rules on accounting for goodwill and other intangible
assets beginning in the first quarter of 2002. Application of the
nonamortization provisions of the Statement is expected to result in a decrease
in net loss of $8.7 million in 2002 and $5.3 million in 2003. During 2002, we
will perform the first of the required impairment tests of goodwill and
indefinite lived intangible assets as of January 1, 2002 and have not yet
determined what the effect of these tests will be on the earnings and our
financial position.

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<PAGE>

         Net Interest Income

Net interest income represents income earned on our cash, cash equivalents and
marketable securities net of interest expense. Net interest income decreased
from $4.4 million and $10.8 million in the three and nine months ended September
30, 2000 to $3.2 million and $10.6 million in the comparable periods of 2001.
This decrease was due to lower average balances of cash, cash equivalents and
marketable securities.

Liquidity and Capital Resources

Since inception, we have financed our operations primarily through private
placements and public offerings of equity securities, receiving aggregate
consideration from such sales totaling $302.5 million and research and
development funding from collaborators and government grants totaling
approximately $70.1 million. As of September 30, 2001, we had $244.8 million in
cash, cash equivalents and investments.

Our operating activities used cash of $7.4 million in the nine months ended
September 30, 2000 and $9.7 million in the nine months ended September 30, 2001.
Uses of cash in operating activities were primarily to fund net operating
losses.

Net cash used in investing activities was $84.7 million in the nine months ended
September 30, 2000 and $46.3 million in the nine months ended September 30,
2001. The cash used during the nine months ended September 30, 2000 and 2001
primarily represented purchases of available-for-sale securities. This was
partially offset by the maturities and sale of available-for-sale securities.

Additions of property and equipment were $2.5 million in the nine months ended
September 30, 2000 and $6.6 million in the nine months ended September 30, 2001.
The increase is primarily due to the expansion of our offices and laboratories
in Redwood City, CA as well as new equipment purchased at Maxygen ApS. We expect
to continue to make significant investments in the purchase of property and
equipment to support our expanding operations. We may use a portion of our cash
to acquire or invest in complementary businesses, products or technologies, or
to obtain the right to use such complementary technologies.

Financing activities provided cash of $138.9 million in the nine months ended
September 30, 2000 and $1.3 million in the nine months ended September 30, 2001.
The 2000 amount primarily consists of the net proceeds received from the sale of
common stock in a follow-on public offering in March 2000. The cash provided in
the nine months ended September 30, 2001 was primarily from the proceeds of the
sale of common stock in connection with our Employee Stock Purchase Plan, our
matching contribution for the 401(k) Plan, and the exercise of stock options by
employees. This was partially offset by payments on equipment financing
obligations of $389,000.

Assuming our research efforts for existing collaborations are expended for the
full research term, as of September 30, 2001 we have total committed funding of
$131.5 million, of which approximately $100.6 million is from our collaborators
and $30.9 million is from government funding. Of these committed funds, we have
$61.4 million remaining to be received over the next four years. In addition,
potential milestone payments from our existing collaborations could exceed
$295.8 million based on the accomplishment of specific performance criteria, and
we may earn royalties on product sales. In general, the obligation of our
corporate collaborators to provide research funding cannot be terminated by
either party before the end of the research term unless there has been a
material breach of contract or either party has become bankrupt or insolvent. In
the case of such an event, the agreement specifies the rights, if any, that each
party will retain.

We believe that our current cash, cash equivalents, short-term investments and
long-term investments together with funding received from collaborators and
government grants will be sufficient to satisfy our anticipated cash needs for
working capital and capital expenditures for at least the next 12 months.
However, it is possible that we will seek additional financing within this
timeframe. We may raise additional funds through public or private financing,
collaborative relationships or other arrangements. Additional funding, if
sought, may not be available on terms favorable to us. Further, any additional
equity financing may be dilutive to stockholders, and debt financing, if
available, may involve restrictive covenants. Our failure to raise capital when
needed may harm our business and operating results.

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   RISKS FACTORS THAT MAY AFFECT RESULTS OF OPERATIONS AND FINANCIAL CONDITION

You should carefully consider the risks described below, together with all of
the other information included in this report, in considering our business and
prospects. The risks and uncertainties described below are not the only ones
facing Maxygen. Additional risks and uncertainties not presently known to us or
that we currently deem immaterial also may impair our business operations. If
any of the following risks actually occur, our business could be harmed. In such
case, the trading price of our common stock could decline, and you may lose all
or part of your investment.

We Have a History of Net Losses. We Expect to Continue to Incur Net Losses and
We May Not Achieve or Maintain Profitability.

We have incurred net losses since our inception, including a net loss of
approximately $59.6 million for the year ended December 31, 2000 and $33.5
million for the nine months ended September 30, 2001. As of September 30, 2001,
we had an accumulated deficit of approximately $117.3 million. We expect to have
increasing net losses and negative cash flow for at least the next several
years. The size of these net losses will depend, in part, on the rate of growth,
if any, in our contract revenues and on the level of our expenses. To date, we
have derived all our revenues from collaborations and grants and expect to do so
for at least the next several years. Revenues from collaborations and grants are
uncertain because our existing agreements have fixed terms and because our
ability to secure future agreements will depend upon our ability to address the
needs of our potential future collaborators. We expect to spend significant
amounts to fund research and development and enhance our core technologies. As a
result of our acquisition of Maxygen ApS, we expect costs to increase further
due to expanded operations and costs associated with operating in multiple
international locations. As a result, we expect that our operating expenses will
increase significantly in the near term and, consequently, we will need to
generate significant additional revenues to achieve profitability. Even if we do
achieve profitability, we may not be able to sustain or increase profitability
on a quarterly or annual basis.

Commercialization of Our Technologies Depends On Collaborations With Other
Companies. If We Are Unable to Find Collaborators in the Future, We May Not Be
Able to Develop Our Technologies or Products.

Since we do not currently possess the resources necessary to develop and
commercialize potential products that may result from our technologies, or the
resources to complete any approval processes that may be required for these
products, we must enter into collaborative arrangements to develop and
commercialize products. We have entered into collaborative agreements with other
companies to fund the development of certain new products for specific purposes.
These contracts expire after a fixed period of time. If they are not renewed or
if we do not enter into new collaborative agreements, our revenues will be
reduced and our products may not be commercialized.

We have limited or no control over the resources that any collaborator may
devote to our products. Any of our present or future collaborators may not
perform their obligations as expected. These collaborators may breach or
terminate their agreement with us or otherwise fail to conduct their
collaborative activities successfully and in a timely manner. Further, our
collaborators may elect not to develop products arising out of our collaborative
arrangements or devote sufficient resources to the development, manufacture,
marketing or sale of these products. If any of these events occur, we may not be
able to develop our technologies or commercialize our products.

We Are an Early Stage Company Deploying Unproven Technologies. If We Do Not
Develop Commercially Successful Products, We May Be Forced to Cease Operations.

You must evaluate us in light of the uncertainties and complexities affecting an
early stage biotechnology company. Our proprietary technologies are new and in
the early stage of development. We may not develop products that prove to be
safe and efficacious, meet applicable regulatory standards, are capable of being
manufactured at reasonable costs, or can be marketed successfully.

We may not be successful in the commercial development of products. Successful
products will require significant development and investment, including testing,
to demonstrate their cost-effectiveness before their commercialization. To date,
companies in the biotechnology industry have developed and

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<PAGE>

commercialized only a limited number of products. We have not proven our ability
to develop and commercialize products. We must conduct a substantial amount of
additional research and development before any regulatory authority will approve
any of our products. Our research and development may not indicate that our
products are safe and effective, in which case regulatory authorities may not
approve them. Problems frequently encountered in connection with the development
and utilization of new and unproven technologies and the competitive environment
in which we operate might limit our ability to develop commercially successful
products.

We Intend to Conduct Proprietary Research Programs, and Any Conflicts With Our
Collaborators or Any Inability to Commercialize Products Resulting from This
Research Could Harm Our Business.

An important part of our strategy involves conducting proprietary research
programs. We may pursue opportunities in fields that could conflict with those
of our collaborators. Moreover, disagreements with our collaborators could
develop over rights to our intellectual property. Any conflict with our
collaborators could reduce our ability to obtain future collaboration agreements
and negatively impact our relationship with existing collaborators, which could
reduce our revenues.

Certain of our collaborators could also become competitors in the future. Our
collaborators could develop competing products, preclude us from entering into
collaborations with their competitors, fail to obtain timely regulatory
approvals, terminate their agreements with us prematurely or fail to devote
sufficient resources to the development and commercialization of products. Any
of these developments could harm our product development efforts.

We will either commercialize products resulting from our proprietary programs
directly or through licensing to other companies. We have no experience in
manufacturing and marketing, and we currently do not have the resources or
capability to manufacture products on a commercial scale. In order for us to
commercialize these products directly, we would need to develop, or obtain
through outsourcing arrangements, the capability to manufacture, market and sell
products. We do not have these capabilities, and we may not be able to develop
or otherwise obtain the requisite manufacturing, marketing and sales
capabilities. If we are unable to successfully commercialize products resulting
from our proprietary research efforts, we will continue to incur losses.

We May Encounter Difficulties in Managing Our Growth. These Difficulties Could
Increase Our Losses.

We have experienced rapid and substantial growth that has placed and, if this
growth continues as expected, will continue to place a strain on our human and
capital resources. If we are unable to manage this growth effectively, our
losses could increase. The number of our employees increased from 74 at December
31, 1998 to 143 at December 31, 1999 to 252 at December 31, 2000 to 297 at
September 30, 2001. Our revenues increased from $2.7 million in 1998 to $14.0
million in 1999 to $24.5 million in 2000 and were $22.0 million for the nine
months ended September 30, 2001. Our ability to manage our operations and growth
effectively requires us to continue to expend funds to enhance our operational,
financial and management controls, reporting systems and procedures and to
attract and retain sufficient numbers of talented employees. If we are unable to
implement improvements to our management information and control systems in an
efficient or timely manner, or if we encounter deficiencies in existing systems
and controls, then management may have access to inadequate information to
manage our day-to-day operations. Failure to attract and retain sufficient
numbers of talented employees will further strain our human resources and could
impede our growth and ability to satisfy our obligations under collaboration
agreements. This would reduce our revenue, increase our losses and harm our
reputation in the marketplace.

The Operation of International Locations May Increase Operating Expenses and
Divert Management Attention.

We are expanding internationally. We acquired Maxygen ApS in August 2000, a
Danish biotechnology company, and are now operating with international business
locations. Expansion into an international operational entity will require
additional management attention and resources. We have limited experience in
localizing our operations and in conforming our operations to local cultures,
standards and policies. We may have to compete with local companies who
understand the local situation better than we

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do. We may not be successful in expanding into international locations or in
generating revenues from foreign operations. Even if we are successful, the
costs of operating internationally are expected to exceed our international
revenues for at least the next several years. As we continue to expand
internationally, we are subject to risks of doing business internationally,
including the following:

     .    regulatory requirements that may limit or prevent the offering of our
          products in local jurisdictions;

     .    government limitations on research and/or research involving
          genetically engineered products or processes;

     .    difficulties in staffing and managing foreign operations;

     .    longer payment cycles, different accounting practices and problems in
          collecting accounts receivable;

     .    cultural non-acceptance of genetic manipulation and genetic
          engineering; and

     .    potentially adverse tax consequences.

To the extent we expand our international operations and have additional
portions of our international revenues denominated in foreign currencies, we
also could become subject to increased difficulties in collecting accounts
receivable and risks relating to foreign currency exchange rate fluctuations.

Acquisitions Could Result in Dilution, Operating Difficulties and Other Harmful
Consequences.

If appropriate opportunities present themselves, we intend to acquire businesses
and technologies that complement our capabilities. The process of integrating
any acquisition may create unforeseen operating difficulties and expenditures
and is itself risky. The areas where we may face difficulties include:

     .    diversion of management time (both ours and that of the acquired
          company) from focus on operating the businesses to issues of
          integration during the period of negotiation through closing and
          further diversion of such time after closing;

     .    decline in employee morale and retention issues resulting from changes
          in compensation, reporting relationships, future prospects, or the
          direction of the business;

     .    the need to integrate each company's accounting, management
          information, human resource and other administrative systems to permit
          effective management and the lack of control if such integration is
          delayed or not implemented; and

     .    the need to implement controls, procedures and policies appropriate
          for a larger public company in companies that before acquisition had
          been smaller, private companies.

We do not have extensive experience in managing this integration process.
Moreover, the anticipated benefits of any or all of these acquisitions may not
be realized.

Future acquisitions could result in potentially dilutive issuances of equity
securities, the incurrence of debt, contingent liabilities or amortization
expenses related to goodwill and other intangible assets, any of which could
harm our business. Future acquisitions may require us to obtain additional
equity or debt financing, which may not be available on favorable terms or at
all. Even if available, this financing may be dilutive.

Since Our Technologies Can Be Applied to Many Different Industries, If We Focus
Our Efforts on Industries That Fail to Produce Viable Product Candidates, We May
Fail to Capitalize on More Profitable Areas.

We have limited financial and managerial resources. Since our technologies may
be applicable to numerous, diverse industries, we must prioritize our
application of resources to discrete efforts. This requires us to focus on
product candidates in selected industries and forego efforts with regard to
other products and industries. Our decisions may not produce viable commercial
products and may divert our resources from more profitable market opportunities.

Public Perception of Ethical and Social Issues May Limit the Use of Our
Technologies, Which Could Reduce Our Revenues.

Our success will depend in part upon our ability to develop products discovered
through our technologies. Governmental authorities could, for social or other
purposes, limit the use of genetic processes or prohibit the practice of our
directed molecular evolution technologies or other technologies. Ethical and
other

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concerns about our directed molecular evolution technologies or other
technologies, particularly the use of genes from nature for commercial purposes,
and products resulting therefrom, could adversely affect their market
acceptance.

If the Public Rejects Genetically Engineered Products, We Will Have Less Demand
for Our Products.

The commercial success of our potential products will depend in part on public
acceptance of the use of genetically engineered products including drugs, plants
and plant products. Claims that genetically engineered products are unsafe for
consumption or pose a danger to the environment may influence public attitudes.
Our genetically engineered products may not gain public acceptance. Negative
public reaction to genetically modified organisms and products could result in
greater government regulation of genetic research and resultant products,
including stricter labeling laws or regulations, and could cause a decrease in
the demand for our products.

The subject of genetically modified organisms has received negative publicity in
Europe and the United States, which has aroused public debate. The adverse
publicity could lead to greater regulation and trade restrictions on genetic
research and the resultant agricultural and other products could be subject to
greater domestic or international regulation. Such regulation and restrictions
could cause a decrease in the demand for our products.

Many Potential Competitors Who Have Greater Resources and Experience Than We Do
May Develop Products and Technologies That Make Ours Obsolete.

The biotechnology industry is characterized by rapid technological change, and
the area of gene research is a rapidly evolving field. Our future success will
depend on our ability to maintain a competitive position with respect to
technological advances. Rapid technological development by others may result in
our products and technologies becoming obsolete.

We face, and will continue to face, intense competition from organizations such
as large and small biotechnology companies, as well as academic and research
institutions and government agencies that are pursuing competing technologies
for modifying DNA and proteins. These organizations may develop technologies
that are alternatives to our technologies. Further, our competitors in the
directed molecular evolution field may be more effective at implementing their
technologies to develop commercial products. Some of these competitors have
entered into collaborations with leading companies within our target markets to
produce commercial products.

Any products that we develop through our technologies will compete in multiple,
highly competitive markets. Most of the organizations competing with us in the
markets for such products have greater capital resources, research and
development and marketing staffs and facilities and capabilities, and greater
experience in modifying DNA and proteins, obtaining regulatory approvals,
manufacturing products and marketing.

Accordingly, our competitors may be able to develop technologies and products
more easily, which would render our technologies and products and those of our
collaborators obsolete and noncompetitive.

Any Inability to Adequately Protect Our Proprietary Technologies Could Harm Our
Competitive Position.

Our success will depend in part on our ability to obtain patents and maintain
adequate protection of our intellectual property for our technologies and
products in the U.S. and other countries. If we do not adequately protect our
intellectual property, competitors may be able to practice our technologies and
erode our competitive advantage. The laws of some foreign countries do not
protect proprietary rights to the same extent as the laws of the U.S., and many
companies have encountered significant problems in protecting their proprietary
rights in these foreign countries. These problems can be caused by, for example,
a lack of rules and processes for defending intellectual property rights.

The patent positions of biopharmaceutical and biotechnology companies, including
our patent positions, are generally uncertain and involve complex legal and
factual questions. We will be able to protect our proprietary rights from
unauthorized use by third parties only to the extent that our proprietary
technologies

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are covered by valid and enforceable patents or are effectively maintained as
trade secrets. We will apply for patents covering our technologies and products
as we deem appropriate. However, we may not obtain patents on all inventions
that we seek to protect with patents, and any patents we obtain may be
challenged and may be narrowed in scope or extinguished as a result of such
challenges. Our existing patents and any future patents we obtain may not be
sufficiently broad to prevent others from practicing our technologies. Others
may independently develop similar or alternative technologies or design around
our patented technologies. Furthermore, our existing patents and any future
patents we obtain may not be sufficiently broad to prevent others from
developing competing products. In addition, others may challenge or invalidate
our patents, or our patents may fail to provide us with any competitive
advantages.

We rely upon trade secret protection for our confidential and proprietary
information. We have taken security measures to protect our proprietary
information. These measures may not provide adequate protection for our trade
secrets or other proprietary information. We seek to protect our proprietary
information by entering into confidentiality agreements with employees,
collaborators and consultants. Nevertheless, employees, collaborators or
consultants may still disclose or misuse our proprietary information, and we may
not be able to meaningfully protect our trade secrets. In addition, others may
independently develop substantially equivalent proprietary information or
techniques or otherwise gain access to our trade secrets.

Litigation or Other Proceedings or Third Party Claims of Intellectual Property
Infringement Could Require Us to Spend Time and Money and Could Shut Down Some
of Our Operations.

Our commercial success depends in part on neither infringing patents nor
proprietary rights of third parties, nor breaching any licenses that we have
entered into with regard to our technologies and products. Others have filed,
and in the future are likely to file, patent applications covering genes or gene
fragments that we may wish to utilize with our proprietary technologies, or
products that are similar to products developed with the use of our technologies
or alternative methods of generating gene diversity. If these patent
applications result in issued patents and we wish to use the claimed technology,
we would need to obtain a license from the third party.

Third parties may assert that we are employing their proprietary technology
without authorization. In addition, third parties may obtain patents in the
future and claim that use of our technologies infringes these patents. We could
incur substantial costs and diversion of the time and attention of management
and technical personnel in defending ourselves against any of these claims or
enforcing our patents or other intellectual property rights against others.
Furthermore, parties making claims against us may be able to obtain injunctive
or other equitable relief that could effectively block our ability to further
develop, commercialize and sell products, and such claims could result in the
award of substantial damages against us. In the event of a successful claim of
infringement against us, we may be required to pay damages and obtain one or
more licenses from third parties. We may not be able to obtain these licenses at
a reasonable cost, if at all. In that event, we could encounter delays in
product introductions while we attempt to develop alternative methods or
products or be required to cease commercializing effected products.

We routinely monitor the public disclosures of other companies operating in our
industry regarding their technological development efforts. If we determine that
these efforts violate our intellectual property or other rights, we intend to
take appropriate action, which could include litigation. Any action we take
could result in substantial costs and diversion of management and technical
personnel. Furthermore, the outcome of any action we take to protect our rights
may not be resolved in our favor.

In early 2000, we announced that we initiated an arbitration proceeding against
Enchira Biotechnology Corporation (then known as Energy Biosystems Corporation)
in connection with Enchira's claim that it had developed a "new gene shuffling"
technology. We alleged that Enchira had breached the confidentiality provisions
and certain other terms of the Development and License Agreement entered into by
Enchira and Maxygen in 1997, pursuant to which we disclosed confidential
information regarding our MolecularBreeding directed molecular evolution
technologies to Enchira. An arbitration hearing was held in November 2000 and on
March 8, 2001 we announced that the arbitrator had found that Enchira had
breached three separate provisions of the Development and License Agreement. The
arbitrator found that the gene shuffling technology that Enchira calls Rachitt,
and claims as its own, "was derived from Maxygen's technologies and has no
notable or significant distinctions from those technologies" and that "Maxygen
is the exclusive owner of the gene shuffling technology contained in Rachitt".
The arbitrator

                                       19

<PAGE>

also found that Enchira had misused our confidential information. There were
further arbitration proceedings and on November 5, 2001 we announced the remedy
determined by the arbitrator. The arbitrator awarded us an injunction barring
Enchira from using, practicing, licensing or selling Rachitt technology until
2017. The arbitrator further enjoined Enchira from using, practicing, licensing
or selling certain high throughput screening technology based on our
technologies for three years. The arbitrator also ordered Enchira to reimburse
Maxygen for its attorneys fees and pay all costs of conducting the arbitration.

If We Lose Key Personnel or Are Unable to Attract and Retain Additional
Personnel We May Be Unable to Pursue Collaborations or Develop Our Own Products.

We are highly dependent on the principal members of our management and
scientific staff, the loss of whose services might adversely impact the
achievement of our objectives. In addition, recruiting and retaining qualified
scientific personnel to perform future research and development work will be
critical to our success. We do not currently have sufficient executive
management personnel to execute fully our business plan. There is currently a
shortage of skilled executives, which is likely to continue. As a result,
competition for skilled personnel is intense, and the turnover rate can be high.
Although we believe we will be successful in attracting and retaining qualified
personnel, competition for experienced scientists from numerous companies and
academic and other research institutions may limit our ability to do so on
acceptable terms. Failure to attract and retain personnel could prevent us from
pursuing collaborations or developing our products or core technologies.

Our planned activities will require additional expertise in specific industries
and areas applicable to the products developed through our technologies. These
activities will require the addition of new personnel, including management, and
the development of additional expertise by existing management personnel. The
inability to acquire these services or to develop this expertise could impair
the growth, if any, of our business.

We Will Need Additional Capital in the Future. If Additional Capital is Not
Available, We Will Have to Curtail or Cease Operations.

Our future capital requirements will be substantial and will depend on many
factors including payments received under collaborative agreements and
government grants, the progress and scope of our collaborative and independent
research and development projects, the effect of any acquisitions, and the
filing, prosecution and enforcement of patent claims.

Changes may also occur that would consume available capital resources
significantly sooner than we expect. We may be unable to raise sufficient
additional capital. If we fail to raise sufficient funds, we will have to
curtail or cease operations. We anticipate that existing cash and cash
equivalents and income earned thereon, together with anticipated cash flows from
operations, will enable us to maintain our currently planned operations for at
least the next 12 months. If our capital resources are insufficient to meet
future capital requirements, we will have to raise additional funds to continue
the development of our technologies and complete the commercialization of
products, if any, resulting from our technologies.

Some of Our Programs Depend on Government Grants, Which May Be Withdrawn. The
Government Has License Rights to Technology Developed With Its Funds.

We have received and expect to continue to receive funds under various U.S.
government research and technology development programs. The government may
reduce funding in the future for a number of reasons. For example, some programs
are subject to a yearly appropriations process in Congress. Additionally, we may
not receive funds under existing or future grants because of budgeting
constraints of the agency administering the program. There can be no assurance
that we will receive the entire funding under our existing or future grants.

Our grants provide the U.S. government a non-exclusive, non-transferable,
paid-up license to practice for or on behalf of the U.S. inventions made with
federal funds. If the government exercises these rights, the U.S. government
could use these inventions and our potential market could be reduced.

                                       20

<PAGE>

Our Potential Therapeutic Products Are Subject to a Lengthy and Uncertain
Regulatory Process. If Our Potential Products Are Not Approved, We Will Not Be
Able to Commercialize Those Products.

The Food and Drug Administration must approve any vaccine or therapeutic product
before it can be marketed in the U.S. Before we can file a new drug application
or biologic license application with the FDA, the product candidate must undergo
extensive testing, including animal and human clinical trials, which can take
many years and require substantial expenditures. Data obtained from such testing
are susceptible to varying interpretations that could delay, limit or prevent
regulatory approval. In addition, changes in regulatory policy for product
approval during the period of product development and regulatory agency review
of each submitted new application or product license application may cause
delays or rejections. The regulatory process is expensive and time consuming.
The regulatory agencies of foreign governments must also approve our therapeutic
products before the products can be sold in those other countries.

Because our products involve the application of new technologies and may be
based upon new therapeutic approaches they may be subject to substantial review
by government regulatory authorities and government regulatory authorities may
grant regulatory approvals more slowly for our products than for products using
more conventional technologies. We have not submitted an application to the FDA
or any other regulatory authority for any product candidate, and neither the FDA
nor any other regulatory authority has approved any therapeutic product
candidate developed with our MolecularBreeding directed molecular evolution
technologies for commercialization in the U.S. or elsewhere. We may not be able
to, or our collaborators may not be able to, conduct clinical testing or obtain
the necessary approvals from the FDA or other regulatory authorities for our
products.

Even after investing significant time and expenditures we may not obtain
regulatory approval for our products. Even if we receive regulatory approval,
this approval may entail limitations on the indicated uses for which we can
market a product. Further, once regulatory approval is obtained, a marketed
product and its manufacturer are subject to continual review, and discovery of
previously unknown problems with a product or manufacturer may result in
restrictions on the product, manufacturer or manufacturing facility, including
withdrawal of the product from the market. In certain countries, regulatory
agencies also set or approve prices.

Laws May Limit Our Provision of Genetically Engineered Agricultural Products in
the Future. These Laws Could Reduce Our Ability to Sell These Products.

We may develop genetically engineered agricultural products. The field-testing,
production and marketing of genetically engineered plants and plant products are
subject to federal, state, local and foreign governmental regulation. Regulatory
agencies administering existing or future regulations or legislation may not
allow us to produce and market our genetically engineered products in a timely
manner or under technically or commercially feasible conditions. In addition,
regulatory action or private litigation could result in expenses, delays or
other impediments to our product development programs or the commercialization
of resulting products.

The FDA currently applies the same regulatory standards to foods developed
through genetic engineering as apply to foods developed through traditional
plant breeding. However, genetically engineered food products will be subject to
pre-market review if these products raise safety questions or are deemed to be
food additives. Our products may be subject to lengthy FDA reviews and
unfavorable FDA determinations if they raise questions, are deemed to be food
additives, or if the FDA changes its policy.

The FDA has also announced in a policy statement that it will not require that
genetically engineered agricultural products be labeled as such, provided that
these products are as safe and have the same nutritional characteristics as
conventionally developed products. The FDA may reconsider or change its labeling
policies, or local or state authorities may enact labeling requirements. Any
such labeling requirements could reduce the demand for our products.

The U.S. Department of Agriculture prohibits genetically engineered plants from
being grown and transported except pursuant to an exemption, or under strict
controls. If our future products are not exempted by the USDA, it may be
impossible to sell such products.

                                       21

<PAGE>

Adverse Events in the Field of Gene Therapy May Negatively Impact Regulatory
Approval or Public Perception of Any Gene Therapy Products We or Our
Collaborators May Develop.

Currently, we are not engaged in developing gene therapy products; however, we
may engage in these activities in the future either for our own account or with
collaborators. If we develop, or our collaborators develop, gene therapy
products, these products may encounter substantial delays in development and
approval due to the government regulation and approval process. Adverse events
reported in gene therapy clinical trials may lead to more government scrutiny of
proposed clinical trials of gene therapy products, stricter labeling
requirements for these products and delays in the approval of gene therapy
products for commercial sale.

The commercial success of any potential gene therapy products made by us or our
collaborators will depend in part on public acceptance of the use of gene
therapies for the prevention or treatment of human diseases. Public attitudes
may be influenced by claims that gene therapies are unsafe, and gene therapy
products may not gain the acceptance of the public or the medical community.
Negative public reaction to gene therapy could result in a decrease in demand
for any gene therapy products we or our collaborators may develop.

Health Care Reform and Restrictions on Reimbursements May Limit Our Returns on
Pharmaceutical Products.

Our future products are expected to include pharmaceutical products. Our ability
and that of our collaborators to commercialize pharmaceutical products developed
with our technologies may depend in part on the extent to which reimbursement
for the cost of these products will be available from government health
administration authorities, private health insurers and other organizations.
Third-party payors are increasingly challenging the price of medical products
and services. Significant uncertainty exists as to the reimbursement status of
newly approved health care products, and there can be no assurance that adequate
third party coverage will be available for any product to enable us to maintain
price levels sufficient to realize an appropriate return on our investment in
research and product development.

Destructive Actions By Activists or Terrorists Could Damage Our Facilities,
Interfere with Our Research Activities and Cause Ecological Harm. Any Such
Adverse Events Could Damage Our Ability to Develop Products and Generate
Adequate Revenue to Continue Operations.

Activists and terrorists have recently shown a willingness to damage physical
facilities, equipment and biological materials to publicize and/or further their
ideological causes. Recent events, in New York City and Washington, D.C., shows
that the amount of damage such people are willing and able to cause can
be considerable. Our operations and research activities could be adversely
impacted depending upon the nature and extent of such damage. Such damage could
include damage to our physical facilities, destruction of animals and biological
materials, disruption of our communications and/or data management software used
for research and/or destruction of research records. Any such damage could delay
our research projects and decrease our ability to conduct future research and
development. Damage caused by activist and/or terrorist incidents could also
cause the release of hazardous materials, including chemicals, radioactive and
biological materials, which could damage our reputation in the community. Clean
up of such releases could also be time consuming and costly.

Any significant interruptions in our ability to conduct our business operations
or research and development activities could reduce our revenue and increase our
expenses. Our business interruption insurance may not adequately compensate us
for the impact of interruptions to our business operations.

We Use Hazardous Chemicals and Radioactive and Biological Materials in Our
Business. Any Claims Relating to Improper Handling, Storage or Disposal of These
Materials Could Be Time Consuming and Costly.

Our research and development processes involve the controlled use of hazardous
materials, including chemicals, radioactive and biological materials. Some of
these materials may be novel, including viruses with novel properties and animal
models for the study of viruses. Our operations also produce hazardous waste
products. Some of our work also involves the development of novel viruses and
viral animal models. We cannot eliminate the risk of accidental contamination or
discharge and any resultant injury from these materials. Federal, state and
local laws and regulations govern the use, manufacture, storage,

                                       22

<PAGE>

handling and disposal of these materials. We believe that our current operations
comply in all material respects with these laws and regulations. We could be
subject to civil damages in the event of an improper or unauthorized release of,
or exposure of individuals to, hazardous materials. In addition, claimants may
sue us for injury or contamination that results from our use or the use by third
parties of these materials, and our liability may exceed our total assets.
Compliance with environmental laws and regulations may be expensive, and current
or future environmental regulations may impair our research, development, or
production efforts. We believe that our current operations comply in all
material respects with applicable Environmental Protection Agency regulations.

In addition, certain of our collaborators are working with these types of
hazardous materials in connection with our collaborations. To our knowledge, the
work is performed in accordance with biosafety regulations. In the event of a
lawsuit or investigation, we could be held responsible for any injury caused to
persons or property by exposure to, or release of, these viruses and hazardous
materials. Further, under certain circumstances, we have agreed to indemnify our
collaborators against damages and other liabilities arising out of development
activities or products produced in connection with these collaborations.

Our Collaborations With Outside Scientists May Be Subject to Change, Which Could
Limit Our Access to Their Expertise.

We work with scientific advisors, consultants and collaborators at academic and
other institutions. These scientists are not our employees and may have other
commitments that could limit their availability to us. Although our scientific
advisors generally agree not to do competing work, if a conflict of interest
between their work for us and their work for another entity arises, we may lose
their services. Although our scientific advisors and collaborators sign
agreements not to disclose our confidential information, it is possible that
certain of our valuable proprietary knowledge may become publicly known through
them.

We May Be Sued for Product Liability.

We may be held liable if any product we develop, or any product that is made
with the use or incorporation of, any of our technologies, causes injury or is
found otherwise unsuitable during product testing, manufacturing, marketing or
sale. These risks are inherent in the development of chemical, agricultural and
pharmaceutical products. Although we intend in the future to obtain product
liability insurance, we do not have such insurance currently and this insurance
may be prohibitively expensive, or may not fully cover our potential
liabilities. Inability to obtain sufficient insurance coverage at an acceptable
cost or otherwise to protect against potential product liability claims could
prevent or inhibit the commercialization of products developed by us or our
collaborators. If we are sued for any injury caused by our products, our
liability could exceed our total assets.

Our Stock Price Has Been, and May Continue to Be, Extremely Volatile.

The trading prices of life science company stocks in general, and ours in
particular, have experienced extreme price fluctuations in the last two years.
The valuations of many life science companies without consistent product
revenues and earnings, including ours, are high based on conventional valuation
standards such as price to earnings and price to sales ratios. These trading
prices and valuations may not be sustained. Any negative change in the public's
perception of the prospects of biotechnology or life science companies could
depress our stock price regardless of our results of operations. Other broad
market and industry factors may decrease the trading price of our common stock,
regardless of our performance. Market fluctuations, as well as general political
and economic conditions such as recession or interest rate or currency rate
fluctuations, also may decrease the trading price of our common stock. In
addition, our stock price could be subject to wide fluctuations in response to
factors including the following:

     .    announcements of new technological innovations or new products by us
          or our competitors;
     .    changes in financial estimates by securities analysts;
     .    conditions or trends in the biotechnology and life science industries;
     .    changes in the market valuations of other biotechnology or life
          science companies;
     .    developments in domestic and international governmental policy or
          regulations;
     .    announcements by us or our competitors of significant acquisitions,
          strategic partnerships, joint ventures or capital commitments;

                                       23

<PAGE>

     .    developments in or challenges relating to patent or other proprietary
          rights;
     .    period-to-period fluctuations in our operating results;
     .    future royalties from product sales, if any, by our strategic
          partners; and
     .    sales of our common stock or other securities in the open market.

In the past, stockholders have often instituted securities class action
litigation after periods of volatility in the market price of a company's
securities. If a stockholder files a securities class action suit against us, we
would incur substantial legal fees and our management's attention and resources
would be diverted from operating our business to respond to the litigation.

We Expect that Our Quarterly Results of Operations Will Fluctuate, and This
Fluctuation Could Cause Our Stock Price to Decline.

Our quarterly operating results have fluctuated in the past and are likely to do
so in the future. These fluctuations could cause our stock price to fluctuate
significantly or decline. Some of the factors that could cause our operating
results to fluctuate include:

     .    expiration of research contracts with collaborators or government
          research grants, which may not be renewed or replaced;
     .    the success rate of our discovery efforts leading to milestones and
          royalties;
     .    the timing and willingness of collaborators to commercialize our
          products, which would result in royalties; and
     .    general and industry specific economic conditions, which may affect
          our collaborators' research and development expenditures.

A large portion of our expenses are relatively fixed, including expenses for
facilities, equipment and personnel. Accordingly, if revenues decline or do not
grow as anticipated due to expiration of research contracts or government
research grants, failure to obtain new contracts or other factors, we may not be
able to correspondingly reduce our operating expenses. Failure to achieve
anticipated levels of revenues could therefore significantly harm our operating
results for a particular fiscal period.

Due to the possibility of fluctuations in our revenues and expenses, we believe
that quarter-to-quarter comparisons of our operating results are not a good
indication of our future performance. Our operating results in some quarters may
not meet the expectations of stock market analysts and investors. In that case,
our stock price would likely decline.

Some of Our Existing Stockholders Can Exert Control Over Us, and May Not Make
Decisions that Are in the Best Interests of All Stockholders.

Our executive officers, directors and principal stockholders together control
approximately 34% of our outstanding common stock, including GlaxoSmithKline
plc, which owns approximately 19% of our outstanding common stock. As a result,
these stockholders, if they act together, and GlaxoSmithKline plc by itself, are
able to exert a significant degree of influence over our management and affairs
and over matters requiring stockholder approval, including the election of
directors and approval of significant corporate transactions. In addition, this
concentration of ownership may delay or prevent a change in control of Maxygen
and might affect the market price of our common stock, even when a change may be
in the best interests of all stockholders. In addition, the interests of this
concentration of ownership may not always coincide with our interests or the
interests of other stockholders and accordingly, they could cause us to enter
into transactions or agreements that we would not otherwise consider.

Item 3
Quantitative And Qualitative Disclosures About Market Risk

We are exposed to financial market risks, including changes in interest rates
and foreign currency exchange. To mitigate some of these risks, we utilize
currency forward contracts. We do not use derivative financial instruments for
speculative or trading purposes.

                                       24

<PAGE>

Interest Rate Risk

The primary objective of our investment activities is to preserve principal
while at the same time maximizing yields without significantly increasing risk.
To achieve this objective, we maintain our portfolio of cash equivalents,
short-term and long-term investments in a variety of securities, including
corporate obligations and money market funds. As of September 30, 2001,
approximately 88% of our total portfolio will mature in one year or less, with
the remainder maturing in less than two years.

The following table represents the fair value balance of our cash, cash
equivalents, short-term and long-term investments that are subject to interest
rate risk by year of expected maturity and average interest rates as of
September 30, 2001 (dollars in thousands):

                                                2001             2002
                                             ---------        ----------
        Cash and cash equivalents ........   $  56,684               --
        Average interest rates ...........        3.84%              --

        Short-term investments ...........   $ 157,615               --
        Average interest rates ...........        6.10%              --

        Long-term investments ............          --        $  30,484
        Average interest rates ...........          --             4.84%

We did not hold derivative instruments intended to mitigate interest rate risk
as of September 30, 2001, and we have never held such instruments in the past.
In addition, we had outstanding debt related to equipment financing of $1.4
million as of September 30, 2001, with a range of interest rates of between
11.73% and 12.78%.

Foreign Currency Risk

A substantial majority of our revenue, expense and capital purchasing activities
are transacted in U.S. dollars. However, beginning in 2000 we began to enter
into transactions in Danish kroner. To protect against reductions in value and
the volatility of future cash flows caused by changes in foreign exchange rates,
we have established balance sheet hedging programs. Currency forward contracts
are utilized in these hedging programs. Our hedging programs reduce, but do not
always entirely eliminate, the impact of foreign currency exchange rate
movements. Gains and losses on these foreign currency investments would
generally be offset by corresponding losses and gains on the related hedging
instruments, resulting in negligible net exposure to Maxygen.

At September 30, 2001 we had a total of $5.3 million committed in foreign
currency cash flow forward contracts. The fair value of these forward contracts
at September 30, 2001 is $121,000, which was reflected on the balance sheet as
an asset.

                                       25

<PAGE>

================================================================================
Part II - Other Information

Item 1
Legal Proceedings

Not applicable.

Item 2
Changes in Securities and Use of Proceeds

Recent Sales of Unregistered Securities

On August 4, 2001, we issued an aggregate of 7,412 shares of our common stock in
connection with the acquisition of a license of certain technology. On August
31, 2001 we issued 751 shares of our common stock to a consultant in partial
payment for consulting services rendered to us. On September 30, 2001 we issued
2,839 shares of our common stock to two additional consultants in partial
payment for consulting services rendered to us. There was no underwriter
employed in connection with any of the transactions. The issuances of securities
were deemed to be exempt from registration under the Securities Act of 1933, as
amended (the "Securities Act") in reliance on Section 4(2) of the Securities Act
and Regulation D promulgated thereunder as transactions by an issuer not
involving a public offering. The recipients of the securities represented their
intentions to acquire the securities for investment only and not with a view to
or for sale in connection with any distribution thereof and appropriate legends
were affixed to the share certificates issued in the transactions. The
recipients either received adequate information about us or had access, through
employment or other relationships, to such information. The recipients, either
alone or together with their duly appointed purchaser representatives, were
knowledgeable, sophisticated and experienced in making investment decisions of
this kind and received adequate information about us.

Application of Initial Public Offering Proceeds

The effective date of our first registration statement, filed on Form S-1 under
the Securities Act (No. 333-89413) relating to our initial public offering of
common stock, was December 15, 1999. Net proceeds to us were approximately
$101.0 million. From the effective date through September 30, 2001, the proceeds
were applied toward:

     .    purchases and installation of equipment and build-out of facilities,
          $11.9 million;
     .    repayment of indebtedness, $561,000;
     .    working capital, $23.2 million; and
     .    temporary investments in certificates of deposits, mutual funds and
          corporate debt securities, $65.4 million.

The use of the proceeds from the offering does not represent a material change
in the use of the proceeds described in the registration statement.

Item 3
Defaults Upon Senior Securities

Not applicable.

                                       26



<PAGE>

Item 4
Subimission of Matters to a Vote of Security Holders

Not applicable.

Item 5
Other Information

Not applicable.

Item 6
Exhibits and Reports on Form 8-K

(a)     The following exhibits are filed as part of this report:

                  None.

(b)     There were no reports on Form 8-K filed during the quarter ended
        September 30, 2001.

                                       27



<PAGE>

================================================================================
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.

                                    MAXYGEN, INC.


November 13, 2001                   By:   /s/  Russell J. Howard
                                          --------------------------------------
                                               Russell J. Howard
                                               Chief Executive Officer

November 13, 2001                   By:   /s/  Lawrence Briscoe
                                          --------------------------------------
                                               Lawrence Briscoe
                                               Chief Financial Officer