10-Q

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 June 30, 2004

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  ¨

Indicate by check mark whether the registrant is an accelerated filer (as defined in Rule 12b-2 of the Exchange Act).    Yes  x    No  ¨

As of August 1, 2004, there were 35,189,242 shares of the registrant’s common stock, $0.0001 par value per share, outstanding, which is the only class of common or voting stock of the registrant issued.

MAXYGEN, INC.

FORM 10-Q

QUARTER ENDED JUNE 30, 2004

INDEX

Part I	FINANCIAL INFORMATION
Item 1:	Unaudited Financial Statements:
	Condensed Consolidated Balance Sheets as of December 31, 2003 and June 30, 2004	3
	Condensed Consolidated Statements of Operations for the three and six month periods ended June 30, 2003 and 2004	4
	Condensed Consolidated Statements of Cash Flows for the six month periods ended June 30, 2003 and 2004	5
	Notes to Condensed Consolidated Financial Statements	6
Item 2:	Management’s Discussion and Analysis of Financial Condition and Results of Operations	15
Item 3:	Quantitative and Qualitative Disclosures About Market Risk	31
Item 4:	Controls and Procedures	31
Part II	OTHER INFORMATION
Item 1:	Legal Proceedings	33
Item 2:	Changes in Securities and Use of Proceeds	33
Item 3:	Defaults Upon Senior Securities	33
Item 4:	Submission of Matters to a Vote of Security Holders	33
Item 5:	Other Information	34
Item 6:	Exhibits and Reports on Form 8-K	37
SIGNATURES		38

This report and the disclosures herein include, on a consolidated basis, the continuing business and operations of Maxygen, Inc. and its wholly-owned subsidiaries, Maxygen ApS and Maxygen Holdings Ltd., as well as its majority-owned subsidiary Codexis, Inc., unless, in each case, the context indicates that the disclosure applies only to a named subsidiary. The operations of Verdia, Inc. are reflected as discontinued operations.

We make available on our website all reports filed with the Securities and Exchange Commission, including our reports on Form 10-K, 10-Q and 8-K, as soon as reasonably practicable after they have been filed. Our website is located at www.maxygen.com. Information contained on our website is not a part of this report.

Maxygen is a registered trademark, and MolecularBreeding is a trademark, of Maxygen, Inc. Verdia is a trademark of Verdia, Inc. Codexis is a trademark of Codexis, Inc. The use of the word “partner” and “partnership” does not mean a legal partner or legal partnership.

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PART I – FINANCIAL INFORMATION

ITEM 1

FINANCIAL STATEMENTS

MAXYGEN, INC.

CONDENSED CONSOLIDATED BALANCE SHEETS

(IN THOUSANDS, EXCEPT SHARE AND PER SHARE AMOUNTS)

	December 31, 2003			June 30, 2004
	(Note 1)			(unaudited)
ASSETS
Current assets:
Cash and cash equivalents	$	21,353		$	26,730
Short-term investments		91,116			101,884
Accounts receivable and other receivables		3,528			2,227
Due from Verdia		1,442			978
Prepaid expenses and other current assets		4,868			5,394
Assets of discontinued operations		7,316			4,007
Total current assets		129,623			141,220
Property and equipment, net		11,509			9,563
Goodwill		12,192			12,192
Long-term investments		79,399			47,686
Deposits and other long-term assets		1,346			2,330
Total assets	$	234,069		$	212,991
LIABILITIES AND STOCKHOLDERS’ EQUITY
Current liabilities:
Accounts payable	$	1,599		$	1,746
Accrued compensation		2,439			3,670
Other accrued liabilities		1,904			1,649
Deferred revenue		4,776			3,820
Current portion of equipment financing obligations		55			360
Liabilities of discontinued operations		3,126			2,592
Total current liabilities		13,899			13,837
Deferred revenue		695			1
Non-current equipment financing obligations		—			1,256
Other long-term liabilities		41			14
Minority interest		21,210			21,710
Commitments and contingencies
Stockholders’ equity:
Preferred stock, $0.0001 par value, 5,000,000 shares authorized, no shares issued and outstanding at December 31, 2003 and June 30, 2004		—			—
Common stock, $0.0001 par value, 100,000,000 shares authorized, 34,909,799, and 35,158,293 shares issued and outstanding at December 31, 2003 and June 30, 2004, respectively		3			3
Additional paid-in capital		394,966			396,465
Deferred stock compensation		(251	)		(59	)
Accumulated other comprehensive loss		(1,366	)		(1,864	)
Accumulated deficit		(195,128	)		(218,372	)
Total stockholders’ equity		198,224			176,173
Total liabilities and stockholders’ equity	$	234,069		$	212,991

See accompanying notes.

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MAXYGEN, INC.

CONDENSED CONSOLIDATED STATEMENTS OF OPERATIONS

(IN THOUSANDS, EXCEPT PER SHARE DATA)

(UNAUDITED)

	Three Months ended June 30,						Six Months ended June 30,
	2003			2004			2003			2004
Collaborative research and development revenue	$	3,874		$	3,220		$	11,214		$	7,636
Grant revenue		486			341			1,158			793
Total revenues		4,360			3,561			12,372			8,429
Operating expenses:
Research and development		10,597			11,794			21,468			22,613
General and administrative		3,031			3,503			5,743			6,280
Stock compensation expense (1)		730			131			1,461			282
Amortization of goodwill and other intangible assets		286			—			572			—
Total operating expenses		14,644			15,428			29,244			29,175
Loss from operations		(10,284	)		(11,867	)		(16,872	)		(20,746	)
Interest income and other (expense), net		1,265			697			2,760			1,271
Equity in losses of minority investee		—			(1,000	)		—			(1,000	)
Loss from continuing operations		(9,019	)		(12,170	)		(14,112	)		(20,475	)
Income (loss) from discontinued operations		(985	)		(1,226	)		171			(2,769	)
Net loss		(10,004	)		(13,396	)		(13,941	)		(23,244	)
Subsidiary preferred stock accretion		(319	)		(250	)		(638	)		(500	)
Loss applicable to common stockholders	$	(10,323	)	$	(13,646	)	$	(14,579	)	$	(23,744	)
Basic and diluted earnings (loss) per share:
Continuing operations	$	(0.26	)	$	(0.35	)	$	(0.41	)	$	(0.58	)
Discontinued operations	$	(0.03	)	$	(0.03	)	$		*	$	(0.08	)
Applicable to common stockholders	$	(0.30	)	$	(0.39	)	$	(0.43	)	$	(0.68	)
Shares used in computing basic and diluted earnings (loss) per share		34,365			35,071			34,279			35,006
(1)    Stock compensation expense related to the following:
Research and development	$	568		$	109		$	1,133		$	238
General and administrative		162			22			328			44
	$	730		$	131		$	1,461		$	282

* Less than $0.01 per share.

See accompanying notes.

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MAXYGEN, INC.

CONDENSED CONSOLIDATED STATEMENTS OF CASH FLOWS

(IN THOUSANDS)

(UNAUDITED)

	Six Months ended June 30,
	2003			2004
Operating activities
Loss from continuing operations	$	(14,112	)	$	(20,475	)
Adjustments to reconcile loss from continuing operations to net cash used in operating activities:
Depreciation and amortization		3,112			3,121
Amortization of intangible assets		572			—
Equity in losses of minority investee		—			1,000
Non-cash stock compensation		1,439			479
Common stock issued and stock options granted to consultants for services rendered and for certain technology rights		541			409
Changes in operating assets and liabilities:
Accounts receivable and other receivables		1,223			1,301
Prepaid expenses and other current assets		(282	)		(468	)
Deposits and other assets		29			(984	)
Accounts payable		(7	)		147
Accrued compensation		1,041			1,231
Other accrued liabilities		(1,335	)		(282	)
Deferred revenue		(1,833	)		(1,650	)
Net cash used in operating activities		(9,612	)		(16,171	)
Investing activities
Purchases of available-for-sale securities		(106,235	)		(39,028	)
Maturities of available-for-sale securities		89,352			59,262
Investment in minority investee		—			(1,000	)
Acquisition of property and equipment		(1,644	)		(1,048	)
Net cash provided by (used in) investing activities		(18,527	)		18,186
Financing activities
Repayments under equipment financing obligation		(339	)		(193	)
Borrowings under equipment financing obligation		—			1,754
Equity adjustment from foreign currency translation		(90	)		31
Proceeds from issuance of common stock		1,163			1,306
Net cash provided by financing activities		734			2,898
Cash provided (used) for discontinued operations		(15	)		464
Net increase (decrease) in cash and cash equivalents		(27,420	)		5,377
Cash and cash equivalents at beginning of period		58,600			21,353
Cash and cash equivalents at end of period	$	31,180		$	26,730

See accompanying notes.

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MAXYGEN, INC.

NOTES TO CONDENSED CONSOLIDATED FINANCIAL STATEMENTS

(unaudited)

1. Basis of Presentation and Significant Accounting Policies

Basis of Presentation

The accompanying unaudited condensed consolidated financial statements have been prepared in accordance with generally accepted accounting principles for interim financial information. The information as of June 30, 2004, and for the three months and six months ended June 30, 2003 and June 30, 2004 includes all adjustments (consisting only of normal recurring adjustments) that the management of Maxygen, Inc. (“Maxygen” or the “Company”) believes necessary for fair presentation of the results for the periods presented. The Condensed Consolidated Balance Sheet as of December 31, 2003 has been derived from the audited financial statements at that date.

Results for any interim period are not necessarily indicative of results for any future interim period or for the entire year. The accompanying Condensed Consolidated Financial Statements should be read in conjunction with the financial statements and notes thereto included in the Company’s Annual Report on Form 10-K for the year ended December 31, 2003.

During the three months ended June 30, 2004, the Company agreed to sell Verdia, Inc. (its wholly-owned subsidiary) to Pioneer Hi-Bred International, Inc., a wholly-owned subsidiary of E.I. du Pont de Nemours and Company. This transaction closed on July 1, 2004 (see Note 6). The Company has reclassified the operating results of Verdia to discontinued operations in the consolidated financial statements for the three months and six months ended June 30, 2003 and June 30, 2004 as a result of the Company’s sale of Verdia. The assets, liabilities and results of operations and cash flows of Verdia, Inc. have been reported separately as discontinued operations in the Company’s Condensed Consolidated Financial Statements for all periods presented.

Principles of Consolidation

The consolidated financial statements include the amounts of the Company and its wholly-owned subsidiaries, Maxygen ApS (Denmark) and Maxygen Holdings Ltd. (Cayman Islands), as well as its majority-owned subsidiary, Codexis, Inc.

The Company’s ownership in Codexis was approximately 57% as of June 30, 2004, based upon the voting rights of the issued and outstanding shares of Codexis common and preferred stock. In accordance with EITF Consensus 96-16, “Investor Accounting for an Investee When the Investor Has a Majority of the Voting Interest but the Minority Stockholder or Stockholders Have Certain Approval or Veto Rights” and paragraph 1 of ARB No. 51, “Consolidated Financial Statements”, the Company has included 100% of the net losses of Codexis in the determination of the Company’s consolidated net loss. The Company records minority interest in the Condensed Consolidated Balance Sheets to account for the ownership interest of the minority owners.

On September 13, 2002, Codexis sold $15 million of Codexis convertible preferred stock to investors, of which $5 million was purchased by Maxygen and $10 million was purchased by several unrelated investors. On October 1, 2002, Codexis sold an additional $10 million of convertible preferred stock to unrelated investors. This series of convertible preferred stock included a redemption provision, which provided that the holders of at least a majority of the outstanding shares of this convertible preferred stock (excluding the convertible preferred stock held by Maxygen and its affiliates), voting together as a separate class, may require Codexis to redeem the convertible preferred stock. The redemption price for each share will be payable in cash in exchange for the shares of convertible preferred stock to be redeemed at a sum equal to the applicable original issue price per share plus five percent (5%) of the original issue price per year from the original issue date until the applicable redemption date, plus declared and unpaid dividends. Notice of redemption can be given at any time on or after the fifth anniversary of the original issue date. In connection with these redemption rights, Maxygen has recorded accretion of the redemption premium for the convertible preferred stock, excluding the shares owned by Maxygen, in the amount of $638,000 and $500,000 for the six months ended June 30, 2003 and 2004, respectively. The accretion is recorded as subsidiary preferred stock accretion on the Condensed Consolidated Statement of Operations and as a reduction of additional paid-in capital on the Condensed Consolidated Balance Sheets. Any obligation to make redemption payments is solely an obligation of Codexis and any payments are to be made solely from assets of Codexis. Codexis had 8,101,101 shares of this series of convertible preferred stock outstanding at June 30, 2004, and the

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total redemption value of the outstanding shares was $27.1 million at June 30, 2004; the total redemption value less the redemption value relating to Maxygen’s shares is reflected as minority interest on the Condensed Consolidated Balance Sheets.

The Company’s investment in Avidia Research Institute, formed by the Company and several outside investors in July 2003, in which the Company has an equity interest of 45.9%, is being accounted for under the equity method of accounting.

Reclassifications

Certain previously reported amounts have been reclassified to conform with the current period presentation. These reclassifications, when made, did not have any affect on loss applicable to common stockholders, total assets or total liabilities and stockholders’ equity.

Revenue Recognition

The Company recognizes revenue from multiple element arrangements under collaborative research agreements, which include license payments, research and development services, milestones, and royalties. Revenue arrangements with multiple deliverables are accounted for under the provisions of Emerging Issues Task Force Issue No. 00-21, Revenue Arrangements with Multiple Deliverables, and are divided into separate units of accounting if certain criteria are met, including whether the delivered item has stand-alone value to the customer and whether there is objective and reliable evidence of the fair value of the undelivered items in the arrangement. If applicable, the consideration the Company receives is allocated among the separate units of accounting based on their respective fair values, and the applicable revenue recognition criteria are considered separately for each of the separate units.

Non-refundable up-front payments received in connection with research and development collaboration agreements, including license fees, and 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 payments 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 typically required to perform research and development activities as specified in each respective agreement. Generally, the payments received are not refundable and are 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 research funding 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.

The Company receives royalties from licensees, which are typically based on third-party sales of licensed products or technologies. Royalties are recorded as earned in accordance with the contract terms when third-party results can be reliably measured and collectibility is reasonably assured.

The Company has been awarded grants from the Defense Advanced Research Projects Agency (“DARPA”), National Institute of Standards and Technology-Advanced Technology Program, the U.S. Agency for International Development and the U.S. Army Medical Research and Materiel Command for various research and development projects. The terms of each of these grant agreements are three years with various termination dates, the last of which is June 2005 for existing agreements. Revenue related to grant agreements is recognized as related research and development expenses are incurred.

Loss per common share

Basic and diluted loss per common share has been computed using the weighted-average number of shares of common stock outstanding during the period, less shares subject to repurchase.

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

	Three Months ended June 30,						Six Months ended June 30,
	2003			2004			2003			2004
Loss applicable to common stockholders	$	(10,323	)	$	(13,646	)	$	(14,579	)	$	(23,744	)
Basic and diluted:
Weighted-average shares of common stock outstanding		34,666			35,072			34,611			35,009
Less: weighted-average shares subject to repurchase		(301	)		(1	)		(332	)		(3	)
Weighted-average shares used in computing basic and diluted loss per share		34,365			35,071			34,279			35,006
Basic and diluted loss per common share	$	(0.30	)	$	(0.39	)	$	(0.43	)	$	(0.68	)

The Company has excluded all outstanding stock options, outstanding warrants 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 9,934,519 at June 30, 2003 and 9,792,916 at June 30, 2004. 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 Loss

Comprehensive loss is primarily comprised of net loss, net unrealized gains or losses on available-for-sale securities and foreign currency translation adjustments. Comprehensive loss and its components for the three month and six month periods ended June 30, 2003 and June 30, 2004 were as follows (in thousands):

	Three Months ended June 30,						Six Months ended June 30,
	2003			2004			2003			2004
Net loss	$	(10,004	)	$	(13,396	)	$	(13,941	)	$	(23,244	)
Changes in unrealized gain (loss) on securities available-for-sale		(31	)		(942	)		(84	)		(715	)
Changes in foreign currency translation adjustments		51			64			(298	)		217
Comprehensive loss	$	(9,984	)	$	(14,274	)	$	(14,323	)	$	(23,742	)

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

	December 31, 2003			June 30, 2004
Unrealized gains on securities available-for-sale	$	200		$	9
Unrealized losses on securities available-for-sale		(82	)		(606	)
Foreign currency translation adjustments		(1,484	)		(1,267	)
Accumulated other comprehensive loss	$	(1,366	)	$	(1,864	)

Recent Accounting Pronouncements

In January 2003, the Financial Accounting Standards Board (“FASB”) issued Interpretation No. 46 (or FIN 46), “Consolidation of Variable Interest Entities.” FIN 46 requires a variable interest entity to be consolidated by a company if that company is subject to a majority of the risk of loss from the variable interest entity’s activities or entitled to receive a majority of the entity’s residual returns or both. A variable interest entity is a corporation,

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partnership, trust, or any other legal structures used for business purposes that either (a) does not have equity investors with voting rights or (b) has equity investors that do not provide sufficient financial resources for the entity to support its activities. A variable interest entity often holds financial assets, including loans or receivables, real estate or other property. A variable interest entity may be essentially passive or it may engage in research and development or other activities on behalf of another entity. The consolidation requirements of FIN 46 apply to variable interest entities created after January 31, 2003. In December 2003, the FASB completed deliberations of proposed modifications to FIN 46 (Revised Interpretations) resulting in multiple effective dates based on the nature as well as the creation date of the variable interest entity. Variable interest entities created after January 31, 2003, but prior to January 1, 2004, may be accounted for either based on the original interpretation or the Revised Interpretations. However, the Revised Interpretations must be applied no later than the first quarter of fiscal year 2004. Variable interest entities created after January 1, 2004 must be accounted for under the Revised Interpretations. There has been no material impact to the Company’s financial statements from potential variable interest entities entered into after January 31, 2003 or from the adoption of the deferred provisions in the first quarter of fiscal year 2004.

In November 2003, the Emerging Issues Task Force reached consensus on paragraph 18 of Issue No. 03-01 (“EITF 03-01”), “The Meaning of Other-Than-Temporary Impairment and Its Application to Certain Investments”. Effective for years ending after December 15, 2003, EITF 03-01 requires that certain quantitative and qualitative disclosures should be required for debt and marketable equity securities classified as available-for-sale or held-to-maturity under SFAS No. 115, “Accounting for Certain Investments in Debt and Equity Securities” and SFAS No. 124, “Accounting for Certain Investments Held by Not-for-Profit Organizations” that are impaired at the balance sheet date but for which an other-than-temporary impairment has not been recognized. The provisions of this consensus do not have a significant effect on the Company’s financial position or operating results.

Stock-Based Compensation

The Company accounts for common stock options granted to employees using the intrinsic value method and, thus, recognizes no compensation expense for options granted with exercise prices equal to or greater than the fair value of the Company’s common stock on the date of the grant.

In December 2002, the FASB issued SFAS No. 148, “Accounting for Stock-Based Compensation, Transition and Disclosure.” SFAS No. 148 provides alternative methods of transition for a voluntary change to the fair value based method of accounting for stock-based employee compensation. SFAS No. 148 also requires that disclosures of the pro forma effect of using the fair value method of accounting for stock-based employee compensation be displayed more prominently and in a tabular format. Additionally, SFAS No. 148 requires disclosure of the pro forma effect in interim financial statements. The transition and annual disclosure requirements of SFAS No. 148 are effective for years ending after December 15, 2002.

As permitted under SFAS No. 148, the Company has elected to continue to follow the intrinsic value method in accounting for its stock-based employee compensation arrangement as defined by Accounting Principles Board Opinion (“APB”) No. 25, “Accounting for Stock Issued to Employees”, and related interpretations including FASB Interpretation No. 44, “Accounting for Certain Transactions involving Stock Compensation”, an interpretation of APB No. 25. The following table illustrates the effect on net loss and net loss per common share if the Company had applied the fair value recognition provisions of SFAS No. 123, as amended by SFAS No. 148, using the Black-Scholes option-pricing model, to determine stock-based employee compensation (in thousands except per share data):

	Three Months ended June 30,						Six Months ended June 30,
	2003			2004			2003			2004
Net loss, as reported	$	(10,004	)	$	(13,396	)	$	(13,941	)	$	(23,244	)
Add: Stock based employee compensation cost included in the determination of net loss, as reported		707			89			1,429			177
Deduct: Total stock based employee compensation expense determined under the fair value-based method for all awards		(4,805	)		(2,608	)		(5,673	)		(5,208	)
Pro forma net loss	$	(14,102	)	$	(15,915	)	$	(18,185	)	$	(28,275	)
Net loss per common share
Basic and diluted	$	(0.29	)	$	(0.38	)	$	(0.41	)	$	(0.66	)
Basic and diluted – pro forma	$	(0.41	)	$	(0.45	)	$	(0.53	)	$	(0.81	)

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The Black-Scholes option-pricing model was developed for use in estimating the fair value of traded options that have no restrictions and are fully transferable and negotiable in a free trading market. Black-Scholes does not consider the employment, transfer or vesting restrictions that are inherent in the Company’s employee options. Use of an option valuation model, as required by SFAS No. 123, includes highly subjective assumptions based on long-term predictions, including the expected stock price volatility and average life of each option grant. Because the Company’s employee stock options have characteristics significantly different from those of freely traded options, and because changes in the subjective input assumptions can materially affect the Company’s estimate of the fair value of those options, in the Company’s opinion, existing valuation models, including Black-Scholes, are not reliable single measures and may misstate the fair value of the Company’s employee stock options. The Black-Scholes weighted average estimated fair values of stock options granted during the three months ended June 30, 2003 and 2004 were $4.08 and $4.67 per share, respectively and for the six months ended June 30, 2003 and 2004 were $4.02 and $5.02 per share, respectively.

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 investments. Unrealized gains and losses are reported as accumulated other comprehensive 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 and declines in value deemed to be other than temporary, if any, 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 June 30, 2004 were as follows (in thousands):

	Amortized Cost			Gross Unrealized Gains		Gross Unrealized Losses			Estimated Fair Value
Money market funds	$	25,931		$	—	$	—		$	25,931
Corporate bonds		133,074			—		(601	)		132,473
Commercial paper		17,887			9		—			17,896
Total		176,892			9		(601	)		176,300
Less amounts classified as cash equivalents		(26,730	)		—		—			(26,730	)
Total investments	$	150,162		$	9	$	(601	)	$	149,570

Realized gains or losses on the sale of available-for-sale securities for the three month and six month periods ended June 30, 2003 and June 30, 2004 were insignificant.

At June 30, 2004, the contractual maturities of investments were as follows (in thousands):

	Amortized Cost		Estimated Fair Value
Due within one year	$	102,120	$	101,884
Due after one year		48,042		47,686
	$	150,162	$	149,570

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3. Derivatives and Financial Instruments

The Company addresses certain financial exposures through a program of risk management that includes the use of derivative financial instruments. To date, the Company has only entered into foreign currency forward exchange contracts generally expiring within eighteen months to reduce the effects of fluctuating foreign currency exchange rates on forecasted cash requirements.

All derivatives are recognized on the balance sheet at their fair value. The Company has designated its derivatives as foreign currency cash flow hedges. Changes in the fair value of derivatives that are highly effective as, and that are designated and qualify as, foreign currency cash flow hedges are recorded in other comprehensive income until the associated hedged transaction impacts earnings.

The Company formally documents all relationships between hedging instruments and hedged items, as well as its risk-management objective and strategy for undertaking various hedge transactions. The Company also formally assesses, both at the hedge’s inception and on an ongoing basis, whether the derivatives that are used in hedging transactions are highly effective in offsetting changes in fair values or cash flows of hedged items. When it is determined that a derivative is not highly effective as a hedge or that it has ceased to be a highly effective hedge, the Company discontinues hedge accounting prospectively.

The purpose of the hedging activities is to minimize the effect of foreign currency exchange rate movements on the cash flows related to the Company’s funding of Maxygen ApS. To date, foreign currency contracts are denominated in Danish kroner. At June 30, 2004, the Company had foreign currency contracts outstanding in the form of forward exchange contracts totaling $11.3 million.

4. Litigation

In December 2001 a lawsuit was filed in the U.S. District Court for the Southern District of New York against Maxygen, Inc., certain officers of the Company, and certain underwriters of the Company’s initial public offering and secondary public offering of common stock. The complaint, which alleges claims under Sections 11, 12(a)(2) and 15 of the Securities Act of 1933 and Section 10(b) of the Securities Exchange Act of 1934, is among the so-called “laddering” cases that have been commenced against over 300 companies that had public offerings of securities in 1999 and 2000. The complaint has been consolidated with other laddering claims in a proceeding styled In re Initial Public Offering Securities Litigation, No. 21 MC 92 (SAS), pending before the Honorable Shira A. Scheindlin. In February 2003, the court dismissed the Section 10(b) claim against the officers of the Company; the remainder of the case remains pending.

In June 2003 the Company agreed to the terms of a tentative settlement agreement along with other defendant issuers in In re Initial Public Offering Securities Litigation. The tentative settlement provides that the 309 defendant issuers and their insurers will pay to the plaintiffs $1 billion less any recovery of damages the plaintiffs receive from the defendant underwriters. If the plaintiffs receive over $5 billion in damages from the defendant underwriters, the Company will be entitled to reimbursement of various expenses incurred by the Company as a result of the litigation. As part of the tentative settlement, the Company will assign to the plaintiffs its “excess compensation claims” and certain other of its claims against the defendant underwriters as a result of the alleged actions of the defendant underwriters. The settlement is subject to acceptance by a substantial majority of defendants and execution of a definitive settlement agreement. The settlement is also subject to court approval, which cannot be assured. The Company believes that its portion of the tentative settlement of the litigation, if any, will be covered by existing insurance.

If the settlement is not accepted by the requisite number of defendants or if it does not receive court approval, the Company intends to defend the lawsuit vigorously. However, the litigation is in the preliminary stage, and the Company cannot predict its outcome. The litigation process is inherently uncertain. If the outcome of the litigation is adverse to the Company and if the Company is required to pay significant damages, the Company’s business would be significantly harmed.

From time to time, the Company becomes involved in claims and legal proceedings that arise in the ordinary course of its business. The Company does not believe that the resolution of any such claims will have a material adverse effect on its financial statements.

5. Segment Information

For the period ended June 30, 2003 the Company had four reportable segments: human therapeutics, chemicals, agriculture and all other. However, later in 2003 the Company reorganized into three segments - human therapeutics, chemicals and agriculture. On July 1, 2004 the Company disposed of its agriculture segment (see

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Notes 6 and 7). The Company has determined its reportable operating segments based upon how the business is managed and operated. The accounting policies of the segments described above are the same as those described in Note 1.

Segment Earnings

During the period ended June 30, 2003 the Company evaluated the performance of its operating segments without considering the effects of net interest income and other (expense), amortization of intangibles and stock compensation expense, all of which were managed by corporate headquarters. Later in 2003 the Company began to evaluate its segments on a standalone, fully allocated, basis. Therefore the segment earnings for the three and six months ended June 30, 2003 have been adjusted to be consistent with the 2003 reorganization. Corporate administrative costs are generally allocated based on headcount.

	Human Therapeutics			Chemicals (Codexis)			Maxygen, Inc. Consolidated
(in thousands)
Three months ended June 30, 2003
Segment loss	$	(6,780	)	$	(2,488	)	$	(9,268	)
Stock compensation		(730	)		—			(730	)
Amortization of intangibles		(286	)		—			(286	)
Interest income and other (expense), net		1,203			62			1,265
Subsidiary preferred stock accretion		—			(319	)		(319	)
Loss applicable to common stockholders – continuing operations	$	(6,593	)	$	(2,745	)	$	(9,338	)
Three months ended June 30, 2004
Segment loss	$	(8,361	)	$	(3,375	)	$	(11,736	)
Stock compensation		(120	)		(11	)		(131	)
Interest income and other (expense), net		685			12			697
Equity in minority interests		(1,000	)		—			(1,000	)
Subsidiary preferred stock accretion		—			(250	)		(250	)
Loss applicable to common stockholders – continuing operations	$	(8,796	)	$	(3,624	)	$	(12,420	)
	Human Therapeutics			Chemicals (Codexis)			Maxygen, Inc. Consolidated
(in thousands)
Six months ended June 30, 2003
Segment loss	$	(12,826	)	$	(2,013	)	$	(14,839	)
Stock compensation		(1,461	)		—			(1,461	)
Amortization of intangibles		(572	)		—			(572	)
Interest income and other (expense), net		2,591			169			2,760
Subsidiary preferred stock accretion		—			(638	)		(638	)
Loss applicable to common stockholders – continuing operations	$	(12,268	)	$	(2,482	)	$	(14,750	)
Six months ended June 30, 2004
Segment loss	$	(14,036	)	$	(6,428	)	$	(20,464	)
Stock compensation		(266	)		(16	)		(282	)
Interest income and other (expense), net		1,227			44			1,271
Equity in minority interests		(1,000	)		—			(1,000	)
Subsidiary preferred stock accretion		—			(500	)		(500	)
Loss applicable to common stockholders – continuing operations	$	(14,075	)	$	(6,900	)	$	(20,975	)

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Segment Revenue

Revenues for each operating segment are derived from the Company’s research collaboration agreements and government grants and are categorized based on the industry of the product or technology under development. The following table presents revenues for each reporting segment (in thousands):

	Three months ended June 30,				Six months ended June 30,
	2003		2004		2003		2004
Human therapeutics	$	3,030	$	2,529	$	6,991	$	6,394
Chemicals		1,330		1,032		5,381		2,035
Total revenue – continuing operations	$	4,360	$	3,561	$	12,372	$	8,429

Identifiable Assets

The following table presents indentifiable assets for each reporting segment (in thousands):

	December 31, 2003		June 30, 2004
Human therapeutics	$	206,455	$	192,733
Chemicals		20,298		16,251
Total assets – continuing operations	$	226,753	$	208,984

6. Discontinued Operations

On July 1, 2004 the Company completed the sale of Verdia, its agriculture subsidiary and sole component of its agriculture segment, to Pioneer Hi-Bred International, Inc., a wholly-owned subsidiary of E.I. du Pont de Nemours and Company, for $64 million in cash. Summarized balance sheet information for the discontinued operations is as follows (in thousands):

	December 31, 2003		June 30, 2004
ASSETS
Current assets	$	5,555	$	3,206
Property and equipment, net		935		799
Deposits and other assets		826		2
Assets of discontinued operations	$	7,316	$	4,007
LIABILITIES
Current liabilities	$	2,949	$	2,490
Other liabilities		177		102
Liabilities of discontinued operations	$	3,126	$	2,592

Summary operating results for the discontinued operations is as follows (in thousands):

	Three Months ended June 30,						Six Months ended June 30,
	2003			2004			2003			2004
Collaborative research and development revenue	$	2,067		$	1,291		$	6,180		$	2,721
Collaborative research and development revenue from related party		762			1,274			1,621			2,454
Grant revenue		151			164			311			311
Total revenues		2,980			2,729			8,112			5,486
Operating expenses:
Research and development		3,180			2,922			6,344			6,165
General and administrative		283			242			625			616
Total operating expenses		3,463			3,164			6,969			6,781
Income (loss) from operations of discontinued operations		(483	)		(435	)		1,143			(1,295	)
Interest income and other, net		38			14			68			32
Equity in net loss of joint venture		(540	)		(805	)		(1,040	)		(1,506	)
Income (loss) from discontinued operations	$	(985	)	$	(1,226	)	$	171		$	(2,769	)

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On a fully allocated basis the general and administrative expense includes amounts charged to Verdia by Maxygen for finance, human resources and general legal expenses. These amounts were $274,000 and $603,000 for the three and six months ended June 30, 2003 and $234,000 and $597,000 for the three and six months ended June 30, 2004.

Verdia’s investment in its joint venture with Delta and Pine Land Company called DeltaMax Cotton LLC in which Verdia has an equity interest of 50% is being accounted for under the equity method of accounting. As a result of the Company’s sale of Verdia on July 1, 2004, Verdia’s portion of the DeltaMax loss is included in the income (loss) from discontinued operations on the Condensed Consolidated Statement of Operations and Verdia’s investment in DeltaMax is included in the assets of discontinued operations on the Condensed Consolidated Balance Sheets.

7. Subsequent Event

Sale of Verdia

On July 1, 2004 the Company completed the sale of Verdia, its agriculture subsidiary and sole component of its agriculture segment, to Pioneer Hi-Bred International, Inc., a wholly-owned subsidiary of E.I. du Pont de Nemours and Company, for $64 million in cash. The operating results of Verdia have been reclassified as discontinued operations. The Company expects to record a gain from sale of discontinued operations of approximately $55.6 million in the quarter ending September 30, 2004.

Pfizer

On July 22, 2004, Codexis entered into a multi-year collaborative research agreement and a license agreement with Pfizer, Inc. to discover and develop biocatalysts, and associated processes that use such biocatalysts, in the manufacture of pharmaceutical products for Pfizer. Under the terms of these agreements, Pfizer will provide Codexis an upfront technology access fee and research funding over a multi-year period. Codexis is also eligible to receive milestone payments, a license fee in the event that Pfizer exercises its option to acquire a non-exclusive worldwide license to certain Codexis gene shuffling technologies and royalties.

Concurrent with the execution of the multi-year collaborative research agreement and the license agreement, Codexis and Pfizer also entered into a stock purchase agreement in which Pfizer purchased from Codexis convertible preferred stock for $10 million. With the Pfizer investment, Maxygen’s ownership of Codexis was reduced to 51.7%.

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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, 2003.

Although we believe that the expectations reflected in the forward-looking statements made in this report 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

Executive Summary

We are a leader in the application of directed molecular evolution, a process by which genes are modified for specific commercial uses. Maxygen began operations in March 1997 with the mission to develop important commercial products through the use of biotechnology. Since then, we have established a focus in human therapeutics, particularly optimized protein pharmaceuticals.

Our business model focuses on developing next-generation protein pharmaceuticals that address significant markets, on our own or with partners. We currently have four next-generation protein therapeutic leads in pre-clinical development. The four leads address significant opportunities and deficiencies in first-generation marketed protein products. The four product candidates are: an optimized alpha interferon for the treatment of hepatitis C infection, partnered with Roche; an optimized gamma interferon for the treatment of idiopathic pulmonary fibrosis and other indications, partnered with InterMune; and two leads to which we retain all rights: an optimized beta interferon for the treatment of multiple sclerosis; and an optimized G-CSF for the treatment of neutropenia.

In additional to our focus in human therapeutics, we established two industrial subsidiaries. Our majority-owned subsidiary Codexis focuses on the development of biocatalysis and fermentation processes and products for the pharmaceutical industry. Codexis now has five processes operating at commercial scale, each process generating royalty payments from partners. Codexis also has over 15 potential products and processes in development with partners and in its own research and development pipeline. On July 1, 2004 we completed the sale of Verdia, our agriculture subsidiary, to Pioneer Hi-Bred International, Inc., a wholly-owned subsidiary of E.I. du Pont de Nemours and Company, for cash proceeds of $64 million.

To date, we have generated revenues from research collaborations with pharmaceutical, chemical, agriculture and petroleum companies and from government grants. Moving forward, we anticipate establishing additional strategic alliances. However, as our internal resources and expertise have grown, we have strategically shifted our dependence on collaborative partner funding to advance our products and business to an increased focus on internal product development for greater potential future value capture. We believe that this is an important step in building long-term value in Maxygen. Consistent with this strategic shift, revenue from continuing operations from strategic alliances and government grants decreased from $28.7 million in 2002 to $22.9 in 2003. Our revenues from continuing operations for the six months ended June 30, 2003 were $12.4 million, compared to $8.4 million during the six months ended June 30, 2004. We anticipate that our revenue from continuing operations from strategic alliances and government grants will continue to decrease in 2004 as compared to 2003 to be approximately $15 million to $20 million.

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We continue to maintain a strong cash position in which to fund our expanded internal product development with cash, cash equivalents and marketable securities totaling $176.3 million as of June 30, 2004. Of this amount, $10.9 million is held by Codexis, leaving a balance of approximately $165.4 million for our therapeutics business. In addition, Maxygen received $64 million in cash on July 1, 2004 in consideration for the sale of Verdia.

We have incurred significant losses since our inception. As of June 30, 2004, our accumulated deficit was $218.4 million. We have invested heavily in establishing our proprietary technologies. Our research and development expenses from continuing operations decreased from $50.1 million in 2002 to $44.4 million in 2003 primarily due to reduced headcount as we wound down the funded research terms of our collaborations with Lundbeck and InterMune. Research and development expenses from continuing operations for the six months ended June 30, 2003 were $21.5 million compared to $22.6 million during the six months ended June 30, 2004. Excluding the gain to be recorded in the quarter ending September 30, 2004 from the sale of Verdia, we expect to incur additional operating losses over at least the next several years.

Critical Accounting Policies and Estimates

The preparation of financial statements in conformity with general accepted accounting principles requires management to make estimates and assumptions that affect the amounts reported in the financial statements and accompanying notes. Actual results could differ from those estimates.

We believe there have been no significant changes in our critical accounting policies during the three and six months ended June 30, 2004 as compared to what was previously disclosed in our Annual Report on Form 10-K for the year ended December 31, 2003.

Deferred Compensation

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 related to the deferred compensation amortization on these option grants, which are split between research and development expense and general and administrative expense, as shown in the following table (in thousands):

	Three Months Ended June 30,				Six Months Ended June 30,
	2003		2004		2003		2004
Research and development	$	182	$	67	$	371	$	134
General and administrative		162		22		328		44
Total deferred compensation amortization	$	344	$	89	$	699	$	178

We expect to fully amortize to expense by August 2004 the remaining deferred compensation relating to pre-IPO grants of stock options to employees. Stock compensation expense in connection with the grant of stock options to consultants for the three and six months ended June 30, 2003 and 2004 were insignificant.

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 was amortized over the remaining vesting period of the options, of which $1,000 was expensed in the three months ended June 30, 2003 and $8,000 was expensed in the six months ended June 30, 2003. No amount was expensed in the three or six months ended June 30, 2004 as the amount was fully amortized to expense during 2003. Also in connection with the Maxygen ApS acquisition, Maxygen shares were exchanged for Maxygen ApS shares. For the shares exchanged that had a right of repurchase, we recorded deferred compensation of $13.1 million. This amount was amortized to expense over a three-year graded vesting period. A total of $362,000 was recognized as expense for the three months ended June 30, 2003 and $723,000 was expensed in the six months ended June 30, 2003. No amount was expensed in the three or six months ended June 30, 2004 as the amount was fully amortized to expense during 2003.

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Results of Operations

Revenues

Our total revenues from continuing operations were $4.4 million and $12.4 million in the three and six months ended June 30, 2003 and were $3.6 million and $8.4 million for the comparable periods in 2004. The net decrease in collaborative research and development revenue of $800,000 between the three month periods ended June 30, 2003 and 2004 is primarily due to the decrease in partner funding as the funded research terms of the Company’s collaborations with Lundbeck and ALK-Abelló A/S wound down on schedule, partially offset by additional revenue from our collaboration with Roche commenced in the third quarter of 2003. The net decrease in collaborative research and development revenue of $4.0 million for the six month periods is primarily due to the decrease in partner funding as the funded research terms of the Company’s collaborations with InterMune, Lundbeck and ALK-Abelló A/S wound down on schedule and the receipt in the first quarter of 2003 of a $2.5 million payment from Hercules to terminate our collaboration agreement, partially offset by additional revenue from our collaboration with Roche which commenced in the third quarter of 2003. We have no ongoing obligations related to the payment received from Hercules. The decline in grant revenue during the three and six months ended June 30, 2004 primarily reflects the decrease in activity on our existing grant projects. In 2004, we expect our consolidated revenue from continuing operations to be approximately $15 million to $20 million, consisting of collaboration revenue, grant revenue and royalties on product sales.

Revenues for each operating segment are derived from our research collaboration agreements and government research grants and are categorized based on the industry of the product or technology under development. Results of Codexis, Inc. are shown as Maxygen’s chemicals segment. The following table presents revenues for each operating segment (in thousands).

	Three Months Ended June 30,				Six Months Ended June 30,
	2003		2004		2003		2004
Human therapeutics	$	3,030	$	2,529	$	6,991	$	6,394
Chemicals		1,330		1,032		5,381		2,035
Total revenue	$	4,360	$	3,561	$	12,372	$	8,429

The decrease in revenue for our human therapeutics segment primarily reflects the scheduled winding down of the funded research term of our collaborations with Lundbeck and ALK-Abelló A/S, partially offset by additional revenue from our collaboration with Roche which commenced in the third quarter of 2003. Revenue for our human therapeutics segment for the next several quarters is expected to decline as we as we continue to implement our strategy of concentrating on internally funded research and development and reduce our dependence on partner funded research and development.

The decrease in revenue for our chemicals segment (Codexis) between the six month periods ended June 30, is due to the termination of the Hercules collaboration in the first quarter of 2003, accentuated by the receipt in 2003 of a $2.5 million payment from Hercules to terminate the collaboration. We have no ongoing obligations related to this payment.

Research and Development Expenses

We do not generally track fully burdened research and development costs or capital expenditures by project. However, we estimate, based on full-time equivalent effort, that the percentage of research and development efforts (as measured in hours incurred, which approximates costs) undertaken for ongoing operations for collaborative projects funded by our collaborators and government grants was 26% and 27% for the three and six months ended June 30, 2003 and was 25% and 25% for the comparable periods in 2004. The decreased percentage of efforts on collaborative projects funded by our collaborators and government grants reflects scheduled reduced efforts in the InterMune and Lundbeck collaborations and the termination of the Hercules agreement, partially offset by the commencement of the Roche collaboration. The percentage of research effort (as measured by hours incurred, which approximates costs) undertaken for ongoing operations for our own internally funded research projects was 74% and 73% for the three and six months ended June 30, 2003 and was 75% and 75% for the comparable periods in 2004. Due to the nature of our research and our dependence on our collaborative partners to commercialize the results of the research, we cannot predict with any certainty whether any particular collaboration or research effort will ultimately result in a commercial product and therefore whether we will receive future milestone payments or royalty payments under our various collaborations.

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Most of our human therapeutic and chemical product development programs are at an early stage and may not result in any marketed products. Product candidates that may appear promising at early stages of development may not reach the market for a number of reasons. Human therapeutic product candidates may be found ineffective or cause harmful side effects during clinical trials, may take longer to pass through clinical trials than had been anticipated, may fail to receive necessary regulatory approvals and may prove impracticable to manufacture in commercial quantities at reasonable costs and with acceptable quality. Superior products may also be developed by our competitors. Chemical product candidates may be found ineffective, may cause undesirable side effects or may prove impracticable to manufacture in commercial quantities at reasonable costs and with acceptable quality. Furthermore, it is uncertain which of our internally developed product candidates will be subject to future collaborative arrangements. The participation of a collaborative partner may accelerate the time to completion and reduce the cost to us of a product candidate or it may delay the time and increase the cost to us due to the alteration of our existing strategy. The risks and uncertainties associated with our research and development projects are discussed more fully in the section of this report titled “Risk Factors That May Affect Results of Operations and Financial Condition”. Because of these risks and uncertainties, we cannot predict when or whether we will successfully complete the development of our product candidates or the ultimate product development cost in any particular case.

Our research and development expenses consist primarily of salaries and other personnel-related expenses, facility costs, research consultants and external collaborative research expenses, supplies and depreciation of facilities and laboratory equipment. Research and development expenses for continuing operations increased from $10.6 million and $21.5 million in the three and six months ended June 30, 2003 to $11.8 million and $22.6 million in the comparable periods of 2004. Stock compensation expense related to research and development for continuing operations was $568,000 and $1.1 million for the three and six months ended June 30, 2003 and was $109,000 and $238,000 for the comparable periods of 2004. The decrease in stock compensation expenses was primarily the result of the completion of amortization expense related to deferred compensation for the shares subject to repurchase that were exchanged in connection with the Maxygen ApS acquisition in August 2000 and the deferred compensation related to the Maxygen ApS acquisition. These items of deferred compensation were fully amortized to expense in 2003. In addition, the decrease in stock compensation expenses includes a decrease in amortization of deferred compensation related to pre-IPO grants of stock options to our employees.

We expect research and development expenses for continuing operations to increase during the balance of 2004 as we increase our efforts on internally funded projects and begin moving product candidates into manufacturing and toward clinical trials. We expect to continue to devote substantial resources to research and development and we expect research and development expenses to increase in the next several years if we are successful in advancing our human therapeutic product candidates into clinical trials. To the extent we out-license our human therapeutic product candidates prior to commencement of clinical trials or collaborate with others with respect to clinical trials, increases in research and development expenses for continuing operations may be delayed, reduced or avoided. We intend to manage the level of our expenditures for research and development, including clinical trials, to balance advancing our human therapeutic product candidates against maintaining adequate cash resources for our continuing operations.

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 insurance premiums and professional expenses, such as legal and accounting. General and administrative expenses for continuing operations increased from $3.0 million and $5.7 million for the three and six months ended June 30, 2003 to $3.5 million and $6.3 million in the comparable periods of 2004. The increase in total general and administrative expenses for continuing operations is primarily due to increases in professional fees, regulatory compliance costs and improvements to infrastructure.

We expect general and administrative expenses for continuing operations for the remainder of 2004 will increase modestly as a result of increased professional fees, regulatory compliance costs and improvements to infrastructure.

Amortization of Other Intangible Assets

In connection with the Maxygen ApS acquisition, we allocated $26.2 million to goodwill and other intangible assets. Upon adoption of SFAS 142 in January 2002, we stopped amortizing goodwill and assembled workforce. However, we continued to amortize the purchased core technology over its three year useful life. Such technology was fully amortized to expense by September 2003.

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Interest Income and Other (Expense), net

Interest income and other (expense), net represents income earned on our cash, cash equivalents and marketable securities net of interest expense on our equipment leases and currency transaction gains or losses. Interest income and other (expense), net for continuing operations decreased from $1.3 million in the three months ended June 30, 2003 to $697,000 in the three months ended June 30, 2004. Interest income and other (expense), net for continuing operations decreased from $2.8 million in the six months ended June 30, 2003 to $1.3 million in the six months ended June 30, 2004. The decrease over both the three and six month periods was due to declining interest rates and lower average balances of cash, cash equivalents and marketable securities and foreign exchange transactions related to the funding of our Danish subsidiary Maxygen ApS which include a $406,832 foreign currency gain in the three months ended June 30, 2003, a $11,000 foreign currency loss in the three months ended June 30, 2004, a $834,000 foreign currency gain in the six months ended June 30, 2003 and a $4,000 foreign currency gain in the six months ended June 30, 2004.

Equity in Losses of Minority Investee

Included in our results of operations is equity in losses of minority investee reflecting our share of the net loss of Avidia Research Institute. Avidia Research Institute was formed in July 2003 and is being accounted for under the equity method of accounting. In June 2004, we provided a $1.0 million loan to Avidia. This loan will be converted into equity of Avidia upon a future sale of Avidia equity securities. The loan has an interest rate of 3% per annum. As of June 30, 2004, the Company had recorded losses equal to its investment basis in Avidia and does not currently expect to be recording any additional losses from Avidia in 2004. Maxygen is not obligated to fund Avidia’s operating losses. There were no equity in losses of minority investee during the three and six month periods ended June 30, 2003 as these periods were prior to the formation of Avidia. Equity in losses of minority investee of continuing operations was a $1.0 million loss for the three and six months ended June 30, 2004.

Subsidiary Preferred Stock Accretion

On September 13, 2002, Codexis sold $15 million of Codexis convertible preferred stock to investors, of which $5 million was purchased by Maxygen and $10 million was purchased by several unrelated investors. On October 1, 2002, Codexis sold an additional $10 million of convertible preferred stock to unrelated investors. This series of convertible preferred stock includes a redemption provision, which provides that the holders of at least a majority of the outstanding shares of this convertible preferred stock (excluding the convertible preferred stock held by Maxygen and its affiliates), voting together as a separate class, may require Codexis to redeem the convertible prefered stock. The redemption price for each share will be payable in cash in exchange for the shares of convertible preferred stock to be redeemed at a sum equal to the applicable original issue price per share plus five percent (5%) of the original issue price per year from the original issue date until the applicable redemption date, plus declared and unpaid dividends. Notice of redemption can be given at any time on or after the fifth anniversary of the original issue date. In connection with these redemption rights, we recorded accretion of the redemption premium for the convertible preferred stock, excluding the shares owned by Maxygen, in the amount of $319,000 and $638,000 for the three and six months ended June 30, 2003 and $250,000 and $500,000 for the three and six months ended June 30, 2004. The accretion is recorded as subsidiary preferred stock accretion on the Condensed Consolidated Statement of Operations and as a reduction of additional paid-in capital on the Condensed Consolidated Balance Sheets. Any obligation to make redemption payments is solely an obligation of Codexis and any payments are to be made solely from assets of Codexis.

Recent Accounting Pronouncements

In January 2003, the FASB issued Interpretation No. 46 (or FIN 46), “Consolidation of Variable Interest Entities.” FIN 46 requires a variable interest entity to be consolidated by a company if that company is subject to a majority of the risk of loss from the variable interest entity’s activities or entitled to receive a majority of the entity’s residual returns or both. A variable interest entity is a corporation, partnership, trust, or any other legal structures used for business purposes that either (a) does not have equity investors with voting rights or (b) has equity investors that do not provide sufficient financial resources for the entity to support its activities. A variable interest entity often holds financial assets, including loans or receivables, real estate or other property. A variable interest entity may be essentially passive or it may engage in research and development or other activities on behalf of another entity. The consolidation requirements of FIN 46 apply to variable interest entities created after January 31, 2003. In December 2003, the FASB completed deliberations of proposed modifications to FIN 46 (Revised Interpretations)

19

resulting in multiple effective dates based on the nature as well as the creation date of the variable interest entity. Variable interest entities created after January 31, 2003, but prior to January 1, 2004, may be accounted for either based on the original interpretation or the Revised Interpretations. However, the Revised Interpretations must be applied no later than the first quarter of fiscal year 2004. Variable interest entities created after January 1, 2004 must be accounted for under the Revised Interpretations. There has been no material impact to the Company’s financial statements from potential variable interest entities entered into after January 31, 2003 or from the adoption of the deferred provisions in the first quarter of fiscal year 2004.

In November 2003, the Emerging Issues Task Force reached consensus on paragraph 18 of Issue No. 03-01 (“EITF 03-01”), “The Meaning of Other-Than-Temporary Impairment and Its Application to Certain Investments”. Effective for years ending after December 15, 2003, EITF 03-01 requires that certain quantitative and qualitative disclosures should be required for debt and marketable equity securities classified as available-for-sale or held-to-maturity under SFAS No. 115, “Accounting for Certain Investments in Debt and Equity Securities” and SFAS No. 124, “Accounting for Certain Investments Held by Not-for-Profit Organizations” that are impaired at the balance sheet date but for which an other-than-temporary impairment has not been recognized. The provisions of this consensus do not have a significant effect on our financial position or operating results.

Liquidity and Capital Resources

Since inception, we have financed our continuing 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 $172.0 million. In addition, our majority-owned subsidiary, Codexis, Inc., received $25 million from a private placement of its equity securities, $20 million from third party investors and $5 million from Maxygen. As of June 30, 2004, we had $176.3 million in cash, cash equivalents and marketable securities. This includes $10.9 million of which may only be used for Codexis operations. In addition, on July 1, 2004 we received $64.0 in cash as proceeds from the sale of our agriculture segment, Verdia, Inc.

Net cash used in operating activities for continuing operations was $9.6 million for the six months ended June 30, 2003 and was $16.2 million for the six months ended June 30, 2004. Uses of cash in operating activities for continuing operations were principally to fund operating losses. The increase in cash used in operating activities for continuing operations primarily relates to a smaller net loss for the six months ended June 30, 2003 due to a one-time non-recurring $2.5 million payment from Hercules to terminate our collaborative agreement recognized as revenue in the first quarter of 2003, lower interest income during the six months ended June 30, 2004 and increased equity in losses of minority investee during the six months ended June 30, 2004.

Net cash used in investing activities for continuing operations was $18.5 million for the six months ended June 30, 2003. Net cash provided by investing activities for continuing operations was $18.2 million for the six months ended June 30, 2004. The cash used in investing activities for continuing operations during the six months ended June 30, 2003 primarily represented purchases of available-for-sale securities net of the maturities of available-for-sale securities. The cash provided by investing activities for continuing operations during the six months ended June 30, 2004 was primarily from the maturities of available-for-sale securities.

Additions of property and equipment for continuing operations were $1.6 million for the six months ended June 30, 2003 and were $1.0 million for the six months ended June 30, 2004. We expect to continue to make investments in the purchase of property and equipment to support our operations. We expect to use a portion of our cash to acquire or invest in businesses, products or technologies, or to obtain the right to use such technologies.

Net cash provided for continuing operations by financing activities was $734,000 for the six months ended June 30, 2003 and was $2.9 million for the six months ended June 30, 2004. The cash provided for continuing operations during the six months ended June 30, 2003 was primarily from the proceeds of the sale of common stock in connection with our Employee Stock Purchase Plan and the exercise of stock options by employees, partially offset by payments on equipment financing obligations. The cash provided for continuing operations during the six months ended June 30, 2004 was primarily from the proceeds of $1.8 million from equipment loans entered into by Codexis. In February 2004, Codexis entered into an equipment financing agreement with a financing company for up to $4.8 million of equipment purchases. The financing agreement expires on December 31, 2004. The equipment loans will be repaid over 48 months from the date of each drawdown at an interest rate tied to the prime lending rate at the time of each drawdown. The loans are secured by the related equipment. In connection with this loan agreement, Codexis issued to the lender, a warrant to purchase 46,176 shares of Codexis’ common stock at $0.40 per share. As of June 30, 2004 Codexis had outstanding loan balances totaling $1.6 million. Any obligations under this equipment financing agreement are solely obligations of Codexis and repayments are to be made solely from assets of Codexis.

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Since inception we have received $155.6 million in funding from our collaborators and from government grants, which includes funding received by Verdia prior to its disposition and $3.3 million of deferred revenue from continuing operations to be recognized over the next two years. Approximately $123.9 million was received from our collaborators and $31.7 million was received from government funding. Assuming our research efforts for existing collaborations and grants from continuing operations continue for their full research terms, as of June 30, 2004 we had total committed funding of approximately $11.2 million remaining to be received over the next two years. Potential milestone payments from our existing collaborations from continuing operations could exceed $375 million based on the accomplishment of specific performance criteria. We may also 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. In addition, on July 1, 2004 we received $64.0 million as proceeds from the sale of our agriculture segment, Verdia, Inc.

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 twelve 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.

Discontinued Operations

Included in our results of operations is a loss from discontinued operations (formerly our agriculture segment) of $985,000 for the three months ended June 30, 2003, income from discontinued operations of $171,000 for the six months ended June 30, 2003 and a loss from discontinued operations of $1.2 million and $2.8 million for the three and six months ended June 30, 2004.

Collaborative research and development revenue from discontinued operations was $2.1 million and $6.2 million in the three and six months ended June 30, 2003 and was $1.3 million and $2.7 million in the three and six months ended June 30, 2004. Collaborative research and development revenue from related party from discontinued operations was $762,000 and $1.6 million in the three and six months ended June 30, 2003 and was $1.3 million and $2.5 million in the three and six months ended June 30, 2004. Grant revenue from discontinued operations was $151,000 and $311,000 in the three and six months ended June 30, 2003 and was $164,000 and $311,000 in the three and six months ended June 30, 2004.

Research and development expenses from discontinued operations were $3.2 million and $6.3 million in the three and six months ended June 30, 2003 and were $2.9 million and $6.2 million in the comparable periods of 2004. General and administrative expenses from discontinued operations were $283,000 and $625,000 in the three and six months ended June 30, 2003 and were $242,000 and $616,000 in the comparable periods of 2004.

Interest income and other, net from discontinued operations was $38,000 and $68,000 in the three and six months ended June 30, 2003 and was $14,000 and $32,000 in the comparable periods of 2004. Equity in net loss of joint venture from discontinued operations was $540,000 and $1.0 million in the three and six months ended June 30, 2003 and was $805,000 and $1.5 million in the comparable periods of 2004.

RISK 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.

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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 loss applicable to common stockholders of $33.9 million in 2002 and $33.7 million in 2003. Our loss applicable to common stockholders for the six months ended June 30, 2004 was $23.7 million. As of June 30, 2004, we had an accumulated deficit of $218.4 million. Excluding the gain to be recorded from the sale of Verdia in the quarter ending September 30, 2004, we expect to incur net losses and negative cash flow from operating activities 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 revenues and on the level of our expenses. To date, we have derived substantially all our revenues from collaborations and grants and expect to derive a substantial majority of our revenue from such sources 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 current and potential future collaborators. We expect to spend significant amounts to fund development of products and further research and development to enhance our core technologies. As a result, we expect that our operating expenses will exceed revenues in the near term and we do not expect to achieve profitability during the next several years. If the time required for us to achieve profitability is longer than we anticipate, we may not be able to continue our business.

We Need to Contain Costs in Order to Achieve Profitability.

We are continuing our efforts to contain costs and reduce our expense structure. We believe strict cost containment and expense reductions in the near term are essential if our current funds are to be sufficient to allow us to achieve future profitability. We assess market conditions on an ongoing basis and plan to take appropriate actions as required. If we are not able to effectively contain our costs and achieve an expense structure commensurate with our business activities and revenues, we may have inadequate levels of cash for future operations or for future capital requirements, which could significantly harm our ability to operate the business.

Our Business and Our Ability to Grow Revenues has been Adversely Impacted by the Economic Slowdown and Related Uncertainties Affecting Markets in Which We Operate.

Adverse economic conditions worldwide have contributed to a slowdown in the biotechnology industry and impacted our business resulting in:

• reduced demand for our technology and the products resulting therefrom;

• increased competition for a decreasing number of research and development collaborations and joint ventures; and

• a significant reduction in the ability of biotechnology companies to raise capital.

Recent political and social turmoil in many parts of the world, including actual incidents and potential future acts of terrorism and war, may continue to put pressure on global economic conditions. These political, social and economic conditions and uncertainties make it difficult for Maxygen and our existing and potential collaboration partners to accurately forecast and plan future business activities. This reduced predictability challenges our ability to increase revenues and reach profitability. In particular, it is difficult to develop and implement strategies, sustainable business models and efficient operations, and effectively manage collaboration relationships due to difficult macroeconomic conditions. If the current economic or market conditions continue or further deteriorate, there could be a material adverse impact on our financial position, revenues, results of operations and cash flow.

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, including joint ventures, to develop and commercialize products. We have entered into collaborative agreements and joint ventures with other companies to fund the development of 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 or joint ventures, 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

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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 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 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 potential 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.

Since Our Technologies Can Be Applied to Many Different Potential Products, If We Focus Our Efforts on Potential Products That Fail to Produce Viable Products, 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 potential products, we must prioritize our application of resources to discrete efforts. This requires us to focus on product candidates in selected areas and forego efforts with regard to other products and areas. Our decisions may not produce viable commercial products and may divert our resources from more profitable market opportunities.

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

Our future capital requirements will depend on many factors including payments received under collaborative agreements, joint ventures and government grants, the progress and scope of our collaborative and independent research and development projects, the extent to which we advance products into clinical trials with our own resources, 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. The current difficult economic climate means that the current ability of biotechnology companies to raise capital is severely limited, particularly companies such as Maxygen without human therapeutic product in late clinical development. If we fail to raise sufficient funds, we may have to curtail or cease operations. We anticipate that existing cash and cash equivalents and income earned thereon, together with anticipated revenues from collaborations, joint ventures and grants, will enable us to maintain our currently planned operations for at least the next twelve 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. If adequate funds are not available, we will not be able to successfully execute our business plan.

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.

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Certain of our collaborators could become our 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 allow 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 Do Not Completely Control Codexis, and Codexis May Make Decisions That Are Not in the Best Interests of Maxygen Stockholders.

Codexis operates as an independent subsidiary of Maxygen. While as of June 30, 2004 we owned 57% of Codexis, our representatives do not constitute a majority of the board of directors and thus we do not have control of the operating or other decisions of Codexis. The interests of Codexis and its stockholders may not always coincide with our interests or the interests of our stockholders. Since Maxygen is currently required to consolidate the financial statements of Codexis with its own financial statements, Codexis may enter into agreements or conduct its operations in a manner that could have a direct material adverse impact on our financial statements and results of operations. Since Maxygen and Codexis presently operate from shared facilities, Codexis could conduct its operations in a manner that adversely affects our business or reputation in the community and/or in the biotechnology industry, making it more difficult to operate in the community, secure additional alliances and maintain existing collaborations. This could have an adverse impact on our ability to conduct business.

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

Our ability to manage our operations 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. These requirements were increased as a result of the increasing operational independence of Codexis and Verdia (prior to its sale). At present we provide a number of operational, financial and reporting services to Codexis and Verdia under services agreements. Such services agreements terminate in early 2005 and could lend to excess fixed cost administrative infrastructure. 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 our 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.

Since August 2000, when we acquired Maxygen ApS, a Danish biotechnology company, we have been operating with international business locations. Operation as an international entity requires additional management attention and resources. We have limited experience in operating internationally and in conforming our operations to local cultures, standards and policies. We also must compete with local companies who understand the local situation better than we do. Due to these operational impediments we may have trouble generating revenues from foreign operations. Even if we are successful, the costs of operating internationally are expected to continue to exceed our international revenues for at least the next several years. As we continue to operate 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;

• local legal and governmental limitations on company-wide employee benefit practices, such as the operation of our employee stock option plan in local jurisdictions;

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

• difficulties in staffing and managing foreign operations;

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

• currency exchange risks;

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

• potentially adverse tax consequences.

Legislative Actions, Potential New Accounting Pronouncements and Higher Compliance Costs are Likely to Adversely Impact Our Future Financial Position and Results of Operations.

Future changes in financial accounting standards, including the possibility that we will be required to expense all stock option grants and other stock-based compensation to employees, may cause adverse, unexpected earnings fluctuations and affect our financial position and results of operations. New accounting pronouncements and varying interpretations of such pronouncements have occurred with frequency in the recent past and may occur in the future. In addition we may make changes in our accounting policies in the future. Compliance with changing regulation of corporate governance and public disclosure will also result in additional expenses. Changing laws, regulations and standards relating to corporate governance and public disclosure, including the Sarbanes-Oxley Act of 2002, new SEC regulations and Nasdaq National Market listing requirements, are creating uncertainty for companies such as ours and compliance costs are increasing as a result of this uncertainty and other factors. We are committed to maintaining high standards of corporate governance and public disclosure. As a result, we intend to invest all reasonably necessary resources to comply with evolving standards, and this investment will result in increased general and administrative expenses and may cause a diversion of management time and attention from revenue-generating activities to compliance activities.

If We Elect or Are Required to Account for Employee Stock Options Using the Fair Value Method, it Would Significantly Increase Our Net Loss.

There has been ongoing public debate concerning whether stock options granted to employees should be treated as a compensation expense and, if so, how to properly value such charges. On March 31, 2004, the Financial Accounting Standard Board (FASB) issued an Exposure Draft, Share-Based Payment: an amendment of FASB statements No. 123 and 95, that would require a company to recognize, as an expense, the fair value of stock options and other stock-based compensation to employees beginning in 2005 and subsequent reporting periods. If we elect or are required to record an expense for our stock-based compensation plans using the fair value method as described in the Exposure Draft, we could have significant and ongoing accounting charges. Such charges would significantly increase our net loss and would delay our ability to achieve profitability.

Substantial Sales of Shares May Adversely Impact the Market Price of our Common Stock.

If our stockholders sell substantial amounts of our common stock, including shares issued upon the exercise of outstanding options, the market price of our common stock may decline. Our common stock trading volume is low and thus the market price of our common stock is particularly sensitive to trading volume. Our low trading volume may also make it more difficult for us to sell equity or equity related securities in the future at a time and price that we deem appropriate. Significant sales of our common stock may adversely impact the then-prevailing market price of our common stock.

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

If appropriate opportunities present themselves, we may 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.

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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 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.

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 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, There Will Be Lower 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. 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 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 allowing for meaningfully defending intellectual property rights.

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We will be able to protect our proprietary rights from unauthorized use by third parties only to the extent that our proprietary technologies are covered by valid and enforceable patents or are effectively maintained as trade secrets. The patent positions of biopharmaceutical and biotechnology companies, including our patent positions, are often uncertain and involve complex legal and factual questions. We apply for patents covering our technologies and products as we deem appropriate. However, we may not obtain patents on all inventions for which we seek 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 or from developing competing products. Others may independently develop similar or alternative technologies or design around our patented technologies or 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 ability to develop products depends in part on not infringing patents nor proprietary rights of third parties, and not 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 or corresponding proteins or peptides 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 patented 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 affected products.

We 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.

From time to time, Maxygen becomes involved in claims and legal proceedings that arise in the ordinary course of its business. We do not believe that the resolution of these claims will have a material adverse effect on us.

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. Although we believe we will be successful in attracting and retaining qualified personnel, competition for experienced scientists from

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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.

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 from the U.S. government provide the U.S. government with a non-exclusive, paid-up license to practice for or on behalf of the U.S. government 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.

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 evolution platform 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.

Our Potential Therapeutic Products Are Subject to a Lengthy and Uncertain Development Process. If Approval of Our Potential Products Is Delayed or Potential Products Do Not Perform as Expected, Our Stock Price and Ability to Raise Capital Will be Reduced.

The development and regulatory process for human therapeutic products is long and uncertain. Most product candidates fail before entering clinical trials and most clinical trials do not result in a marketed product. In addition, due to the nature of human therapeutic research and development, the expected timing of product development and initiation of clinical trials and the results of such development and clinical trials are uncertain and subject to change at any point. This uncertainty may result in research delays and product candidate failures and clinical trial delays and failures. Such delays and failures could drastically reduce the price of our stock and our ability to raise capital. Without sufficient capital, we would need to reduce operations and could be forced to cease operations.

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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 payers 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 shown a willingness to injure people and damage physical facilities, equipment and biological materials to publicize and/or further their ideological causes. Recent bombings in Emeryville, CA also show that biotechnology companies could be a specific target of certain groups. Our operations and research activities could be adversely impacted depending upon the nature and extent of such acts. Such damage could include disability or death of our personnel, 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 any 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.

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 and disposal of hazardous materials, including chemicals, infectious disease agents and 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, 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.

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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 and pharmaceutical products. Although we intend in the future to obtain product liability insurance, we do not have such insurance currently. Any such insurance that we seek to obtain 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, and an Investment in Our Stock Could Decline in Value.

The trading prices of life science company stocks in general, and ours in particular, have experienced significant price fluctuations in the last several years. During the twelve-month period ended June 30, 2004, the closing price of our common stock on the Nasdaq National Market ranged from $8.28 to $15.48. The valuations of many life science companies without consistent product revenues and earnings, including ours, are high based on valuation standards such as price to sales ratios and progress in product development and/or clinical trials. Trading prices based on these 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:

• our failure to meet our publicly announce revenue and/or expense projections and/or product development timetables;

• adverse results or delays in preclinical development or clinical trials;

• any decisions to discontinue or delay development programs or clinical trials;

• 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;

• developments in or challenges relating to patent or other proprietary rights; 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.

In December 2001 a lawsuit was filed in the U.S. District Court for the Southern District of New York against Maxygen, Inc., certain officers of the Company, and certain underwriters of the Company’s initial public offering and secondary public offering of common stock. The complaint, which alleges claims under Sections 11, 12(a)(2) and 15 of the Securities Act of 1933 and Section 10(b) of the Securities Exchange Act of 1934, is among the so-called “laddering” cases that have been commenced against a number of companies that had public offerings of securities prior to December 2000. The complaint has been consolidated with other laddering claims in a proceeding styled In re Initial Public Offering Securities Litigation, No. 21 MC 92 (SAS), pending before the Honorable Shira A. Scheindlin. In February 2003, the court dismissed the Section 10(b) claim against the officers of the Company; the remainder of the case remains pending. We believe the lawsuit against Maxygen and its officers is without merit and intend to defend against it vigorously. See also Part II – Item 1 – Legal Proceedings.

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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 30% 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, could 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. This concentration of ownership could also depress our stock price.

ITEM 3

QUANTITATIVE AND QUALITATIVE DISCLOSURES ABOUT MARKET RISK

Market risk management

Our cash flow and earnings are subject to fluctuations due to changes in foreign currency exchange rates, interest rates, the fair value of equity securities held and our stock price. We attempt to limit our exposure to some or all of these market risks through the use of various financial instruments. There were no significant changes in our market risk exposures during the six months ended June 30, 2004. These activities are discussed in further detail in Part II, Item 7A, “Quantitative and Qualitative Disclosures About Market Risk” of our Annual Report on Form 10-K for the year ended December 31, 2003.

ITEM 4

CONTROLS AND PROCEDURES

Quarterly Controls Evaluation and Related CEO and CFO Certifications. Company management, with the participation of our Chief Executive Officer (“CEO”) and Chief Financial Officer (“CFO”), has evaluated the effectiveness of our disclosure controls and procedures (“Disclosure Controls”) as of the end of the period covered by this report.

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Appearing as Exhibits 31.1 and 31.2 of this report are the certifications of our CEO and CFO, which are required in accordance with Rule 13a-14 of the Exchange Act. This Controls and Procedures section includes the information concerning the controls evaluation referred to in the certifications and it should be read in conjunction with the certifications for a more complete understanding of the topics presented.

Definition of Disclosure Controls. Disclosure Controls are controls and procedures designed to ensure that information required to be disclosed in our reports filed under the Exchange Act, such as this report, is recorded, processed, summarized and reported within the time periods specified in the SEC’s rules and forms. Disclosure Controls are also designed to ensure that such information is accumulated and communicated to our management, including our CEO and CFO, as appropriate to allow timely decisions regarding required disclosure. Our Disclosure Controls include components of our internal control over financial reporting (“Internal Controls”), which consists of control processes designed with the objective of providing reasonable assurance that (1) our transactions are properly authorized; (2) our assets are safeguarded against unauthorized or improper use and (3) our transactions are properly recorded and reported, all to permit the preparation of our financial statements in conformity with generally accepted accounting principles.

Limitations on the Effectiveness of Controls. Our management, including our CEO and CFO, does not expect that our Disclosure Controls will prevent all error and all fraud. A control system, no matter how well conceived and operated, can provide only reasonable, not absolute, assurance that the objectives of the control system will be met. Further, the design of a control system must reflect the fact that there are resource constraints, and the benefits of controls must be considered relative to their costs. Because of the inherent limitations in all control systems, no evaluation of controls can provide absolute assurance that all control issues and instances of fraud, if any, within Maxygen have been detected. These inherent limitations include the realities that judgments in decision-making can be faulty, and that breakdowns can occur because of simple error or mistake. Additionally, controls can be circumvented by the individual acts of some persons, by collusion of two or more people, or by management override of the controls. The design of any system of controls also is based in part upon certain assumptions about the likelihood of future events, and there can be no assurance that any design will succeed in achieving its stated goals under all potential future conditions. Over time, controls may become inadequate because of changes in conditions, or deterioration in the degree of compliance with the policies or procedures. Because of the inherent limitations in a cost-effective control system, misstatements due to error or fraud may occur and not be detected.

Scope of the Controls Evaluation. The CEO/CFO evaluation of our Disclosure Controls included a review of the controls’ objectives and design, the controls’ implementation by Maxygen and the effect of the controls on the information generated for use in this report. In the course of the controls evaluation, we sought to identify errors, controls problems or acts of fraud. Elements of our controls are also evaluated on an ongoing basis by personnel in our Finance department. The overall goals of these various evaluation activities are to monitor our Disclosure Controls and to make modifications as necessary. Our intent in this regard is that the Disclosure Controls will be maintained as dynamic systems that change (including with improvements and corrections) as conditions warrant.

Among other matters, we sought in our evaluation to determine whether there were any significant deficiencies or material weaknesses in our Internal Controls, or whether we had identified any acts of fraud involving personnel who have a significant role in our Internal Controls. This information was important both for the controls evaluation generally and because item 5 in the certifications of our CEO and CFO require that the CEO and CFO disclose that information to our Audit Committee and to our independent auditors and to report on related matters in this section of the report.

Conclusions. Based upon the controls evaluation, our CEO and CFO have concluded that our Disclosure Controls were effective as of June 30, 2004 to ensure that material information relating to Maxygen and its consolidated subsidiaries is made known to management, including the CEO and CFO, particularly during the period when our periodic reports are being prepared.

During the fiscal period covered by this report there have been no significant changes in our internal controls over financial reporting or in other factors that could significantly affect our internal controls over financial reporting, including any corrective actions with regard to significant deficiencies and material weaknesses.

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PART II – OTHER INFORMATION

ITEM 1

LEGAL PROCEEDINGS

In December 2001 a lawsuit was filed in the U.S. District Court for the Southern District of New York against Maxygen, Inc., certain officers of the Company, and certain underwriters of the Company’s initial public offering and secondary public offering of common stock. The complaint, which alleges claims under Sections 11, 12(a)(2) and 15 of the Securities Act of 1933 and Section 10(b) of the Securities Exchange Act of 1934, is among the so-called “laddering” cases that have been commenced against over 300 companies that had public offerings of securities in 1999 and 2000. The complaint has been consolidated with other laddering claims in a proceeding styled In re Initial Public Offering Securities Litigation, No. 21 MC 92 (SAS), pending before the Honorable Shira A. Scheindlin. In February 2003, the court dismissed the Section 10(b) claim against the officers of the Company; the remainder of the case remains pending.

In June 2003 the Company agreed to the terms of a tentative settlement agreement along with other defendant issuers in In re Initial Public Offering Securities Litigation. The tentative settlement provides that the 309 defendant issuers and their insurers will pay to the plaintiffs $1 billion less any recovery of damages the plaintiffs receive from the defendant underwriters. If the plaintiffs receive over $5 billion in damages from the defendant underwriters, the Company will be entitled to reimbursement of various expenses incurred by the Company as a result of the litigation. As part of the tentative settlement, the Company will assign to the plaintiffs its “excess compensation claims” and certain other of its claims against the defendant underwriters as a result of the alleged actions of the defendant underwriters. The settlement is subject to acceptance by a substantial majority of defendants and execution of a definitive settlement agreement. The settlement is also subject to court approval, which cannot be assured. The Company believes that its portion of the tentative settlement of the litigation, if any, will be covered by existing insurance.

If the settlement is not accepted by the requisite number of defendants or if it does not receive court approval, the Company intends to defend the lawsuit vigorously. However, the litigation is in the preliminary stage, and the Company cannot predict its outcome. The litigation process is inherently uncertain. If the outcome of the litigation is adverse to the Company and if the Company is required to pay significant damages, the Company’s business would be significantly harmed.

ITEM 2

CHANGES IN SECURITIES AND USE OF PROCEEDS

Recent Sales of Unregistered Securities

On May 8, 2004 we issued a total of 22,907 shares of our common stock to a total of four consultants in partial payment for consulting services rendered to us. There was no underwriter employed in connection with any of the above described 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 upon 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.

ITEM 3

DEFAULTS UPON SENIOR SECURITIES

Not applicable.

ITEM 4

SUBMISSION OF MATTERS TO A VOTE OF SECURITY HOLDERS

We held our Annual Meeting of Stockholders on June 22, 2004. The following is a brief description of each matter voted upon at the meeting and the number of votes cast for, withheld, or against and the number of abstentions with respect to each matter. Each director proposed by the Company was elected and the one management proposal was approved by the stockholders.

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(a) The stockholders reelected the six nominees for the Company’s Board of Directors:

Candidate	Shares Voted For Candidate	Shares Withheld
M.R.C. Greenwood	30,601,654	352,430
Russell J. Howard	30,618,793	335,291
Ernest Mario	30,168,736	785,348
Gordon Ringold	30,222,481	731,603
Isaac Stein	28,138,386	2,815,698
James R. Sulat	30,613,586	340,498

(b) The stockholders ratified the selection of Ernst & Young LLP as independent auditors of the Company for the fiscal year ending December 31, 2004:

Shares voted for	30,693,540
Shares voted against	258,329
Shares abstaining	2,215
Broker non-votes	0

ITEM 5

OTHER INFORMATION

PRO FORMA FINANCIAL INFORMATION

The unaudited pro forma condensed consolidated balance sheet as of June 30, 2004 was derived from the unaudited balance sheet presented elsewhere in this report.

The unaudited pro forma condensed consolidated statement of operations for the year ended December 31, 2003 is presented as if the sale of Verdia had been consummated on January 1, 2003 and excludes the gain on sale of discontinued operations of approximately $55.6 million that will be recorded by the Company during the quarter ending September 30, 2004. The historical results of the Company were derived from its consolidated statement of operations included in its Annual Report on Form 10-K for its fiscal year ended December 31, 2003. The historical results of Verdia were derived from its unaudited December 31, 2003 statement of operations included in Maxygen’s consolidated results.

A pro forma condensed consolidated statement of operations for the six months ended June 30, 2004 has not been presented as the operating results of Verdia have been reflected in the results of the Company presented elsewhere in this report. The results of Verdia were derived from its unaudited June 30, 2004 statement of operations and included in Maxygen’s consolidated results as discontinued operations.

The unaudited pro forma condensed consolidated financial statements have been prepared by the Company management for illustrative purposes only and are not necessarily indicative of the results of operations in future periods or the results that actually would have been realized had the Company divested Verdia during the specified periods. The pro forma adjustments are based on the information available at the time of the preparation of this report. The unaudited pro forma condensed consolidated financial statements, including the notes thereto, are qualified in their entirety by reference to, and should be read in conjunction with, the historical consolidated financial statements of the Company included in its Annual Report on Form 10-K for its year ended December 31, 2003 and the unaudited condensed historical consolidated financial statements of the Company included in this report.

There were material intercompany balances and transactions between Maxygen and Verdia. As of June 30, 2004 Verdia’s liability to Maxygen was $978,000.

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UNAUDITED PRO FORMA CONDENSED CONSOLIDATED BALANCE SHEET

OF MAXYGEN, INC.

As of June 30, 2004

(In Thousands)

	As Reported Maxygen, Inc. Consolidated			Pro Forma Adjustments			Pro Forma Maxygen, Inc. Consolidated
ASSETS
Current assets:
Cash and cash equivalents	$	26,730		$	64,000	(a)	$	90,730
Short term investments		101,884			—			101,884
Other current assets		8,599			—			8,599
Assets of discontinued operations		4,007			(4,007	)(b)		—
Total current assets		141,220			59,993			201,213
Property and equipment, net		9,563			—			9,563
Goodwill and other intangible assets, net		12,192			—			12,192
Long-term investments		47,686			—			47,686
Other assets		2,330			—			2,330
Total assets	$	212,991		$	59,993		$	272,984
LIABILITIES AND STOCKHOLDERS’ EQUITY
Total current liabilities	$	11,245		$	1,341	(c)	$	12,586
Liabilities of discontinued operations		2,592			(2,592	)(d)		—
Long-term obligations		1,271			—			1,271
Minority Interest		21,710			—			21,710
Stockholders’ equity:
Common stock and additional paid-in capital		396,468			350	(e)		396,818
Deferred stock comp. and accumulated other comprehensive income (loss)		(1,923	)		4	(f)		(1,919	)
Accumulated deficit		(218,372	)		5,334	(g)		(157,482	)
					55,556	(h)
Total stockholders’ equity		176,173			61,244			237,417
Total liabilities and stockholders’ equity	$	212,991		$	59,993		$	272,984

See Notes to Unaudited Pro Forma Condensed Consolidated Financial Statements.

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UNAUDITED PRO FORMA CONDENSED CONSOLIDATED STATEMENT

OF OPERATIONS OF MAXYGEN, INC.

For the Year Ended December 31, 2003

(In Thousands, Except per Share Data)

	As Reported Maxygen, Inc.			Less: Verdia			Pro Forma Maxygen, Inc.
Revenues:
Collaborative research and development revenue	$	30,506		$	(9,933	)	$	20,573
Collaborative research and development revenue from related party		3,723			(3,723	)		—
Grant revenue		2,996			(714	)		2,282
Total Revenue		37,225			(14,370	)		22,855
Operating Expenses:
Research and development		56,869			(12,434	)		44,435
General and administrative		12,594			(1,240	)		11,354
Stock compensation expense		1,991			—			1,991
Amortization of goodwill and other intangible assets		698			—			698
Total operating expenses		72,152			(13,674	)		58,478
Loss from operations		(34,927	)		(696	)		(35,623	)
Interest income and other (expense), net		5,374			(121	)		5,253
Equity in net loss of joint venture and minority investee		(2,903	)		2,403			(500	)
Loss from continuing operations		—			—			(30,870	)
Loss from discontinued operations		—			1,586			(1,586	)
Net loss	$	(32,456	)		—		$	(32,456	)
Subsidiary preferred stock accretion		(1,279	)		—			(1,279	)
Loss applicable to common stockholders	$	(33,735	)		—		$	(33,735	)
Basic and diluted loss per share:
Continuing operations	$	—					$	(0.89	)
Discontinued operations	$	—					$	(0.05	)
Applicable to common stockholders	$	(0.98	)				$	(0.98	)
Shares used in computing basic and diluted loss per share		34,519						34,519

See Notes to Unaudited Pro Forma Condensed Consolidated Financial Statements.

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Pro Forma Adjustments

Pro forma adjustments for the balance sheet as of June 30, 2004 are necessary to reflect Maxygen’s balances excluding Verdia’s assets, liabilities and stockholders’ equity and including the cash received from Pioneer, the gain to be recorded by Maxygen, the income tax effect, the stock compensation related to option exercise as part of the transaction and the transaction costs as if the transaction was completed on June 30, 2004.

Pro forma adjustments for the statement of operations for the year ended December 31, 2003 are necessary to reflect Maxygen’s results of operations excluding Verdia and do not include the extraordinary gain on the disposition of Verdia which the Company will record in the quarter ended September 30, 2004.

The pro forma adjustments included in the unaudited pro forma condensed consolidated financial statements are as follows:

(a) Cash proceeds from sale of Verdia to Pioneer

(b) Verdia’s net assets

(c) Estimated income tax expense of $921,000 and transaction costs of $420,000

(d) Verdia’s net liabilities

(e) Stock compensation related to option exercises as part of the transaction

(f) Accumulated other comprehensive income (loss) of Verdia’s held for sale securities

(g) Verdia’s accumulated deficit

(h) Maxygen’s estimated gain on the sale of Verdia

PRE-APPROVAL OF NON-AUDIT SERVICES

During the three month period ended June 30, 2004, the Audit Committee of the Board of Directors approved the following non-audit service to be performed by Ernst & Young LLP: assistance and consultation regarding the availability of tax losses in connection with the sale of Verdia.

The Audit Committee has determined that the rendering of the non-audit service described above by Ernst & Young LLP is compatible with maintaining the auditor’s independence.

ITEM 6

EXHIBITS AND REPORTS ON FORM 8-K

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

31.1 Certification of Chief Executive Officer

31.2 Certification of Chief Financial Officer

32.1 Certification of Chief Executive Officer and Chief Financial Officer pursuant to 18 U.S.C. Section 1350, as adopted pursuant to Section 906 of the Sarbanes-Oxley Act of 2002

(b) The following reports on Form 8-K were filed during the quarter ended June 30, 2004

On April 27, 2004 Maxygen filed a report on Form 8-K (items 7 and 12), attaching thereto a press release reporting its first quarter earnings.

On May 7, 2004 Maxygen filed a report on Form 8-K (item 11), reporting a temporary suspension of trading under its employee benefits plans.

On June 3, 2004 Maxygen filed a report on Form 8-K (item 5), attaching thereto a press release reporting entry into an agreement to sell its agriculture subsidiary, Verdia, Inc.

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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.
August 6, 2004	By:	/s/ Russell J. Howard
		Russell J. Howard
		Chief Executive Officer
August 6, 2004	By:	/s/ Lawrence W. Briscoe
		Lawrence W. Briscoe
		Chief Financial Officer

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EX-31.1

Exhibit 31.1

Certification of Chief Executive Officer

I, Russell J. Howard, certify that:

1. I have reviewed this quarterly report on Form 10-Q of Maxygen, Inc.;

2. Based on my knowledge, this report does not contain any untrue statement of a material fact or omit to state a material fact necessary to make the statements made, in light of the circumstances under which such statements were made, not misleading with respect to the period covered by this report;

3. Based on my knowledge, the financial statements, and other financial information included in this report, fairly present in all material respects the financial condition, results of operations and cash flows of the registrant as of, and for, the periods presented in this report;

4. The registrant’s other certifying officer and I are responsible for establishing and maintaining disclosure controls and procedures (as defined in Exchange Act Rules 13a-15(e) and 15d-15(e)) for the registrant and have:

a) designed such disclosure controls and procedures, or caused such disclosures and procedures to be designed under our supervision, to ensure that material information relating to the registrant, including its consolidated subsidiaries, is made known to us by others within those entities, particularly during the period in which this report is being prepared;

b) evaluated the effectiveness of the registrant’s disclosure controls and procedures and presented in this report our conclusions about the effectiveness of the disclosure controls and procedures, as of the end of the period covered by this report based on such evaluation; and

c) disclosed in this report any change in the registrant’s internal control over financial reporting that occurred during the registrant’s most recent fiscal quarter (the registrant’s fourth fiscal quarter in the case of an annual report) that has materially affected, or is reasonably likely to materially affect, the registrant’s internal control over financial reporting; and

5. The registrant’s other certifying officer and I have disclosed, based on our most recent evaluation of internal control over financial reporting, to the registrant’s auditors and the audit committee of registrant’s board of directors (or persons performing the equivalent functions):

a) all significant deficiencies and material weaknesses in the design or operation of internal control over financial reporting which are reasonably likely to adversely affect the registrant’s ability to record, process, summarize and report financial information; and

b) any fraud, whether or not material, that involves management or other employees who have a significant role in the registrant’s internal controls over financial reporting.

Date: August 6, 2004	/s/ Russell J. Howard
	Russell J. Howard
	Chief Executive Officer

EX-31.2

Exhibit 31.2

Certification of Chief Financial Officer

I, Lawrence W. Briscoe, certify that:

1. I have reviewed this quarterly report on Form 10-Q of Maxygen, Inc.;

2. Based on my knowledge, this report does not contain any untrue statement of a material fact or omit to state a material fact necessary to make the statements made, in light of the circumstances under which such statements were made, not misleading with respect to the period covered by this report;

3. Based on my knowledge, the financial statements, and other financial information included in this report, fairly present in all material respects the financial condition, results of operations and cash flows of the registrant as of, and for, the periods presented in this report;

4. The registrant’s other certifying officer and I are responsible for establishing and maintaining disclosure controls and procedures (as defined in Exchange Act Rules 13a-15(e) and 15d-15(e)) for the registrant and have:

a) designed such disclosure controls and procedures, or caused such disclosures and procedures to be designed under our supervision, to ensure that material information relating to the registrant, including its consolidated subsidiaries, is made known to us by others within those entities, particularly during the period in which this report is being prepared;

b) evaluated the effectiveness of the registrant’s disclosure controls and procedures and presented in this report our conclusions about the effectiveness of the disclosure controls and procedures, as of the end of the period covered by this report based on such evaluation; and

c) disclosed in this report any change in the registrant’s internal control over financial reporting that occurred during the registrant’s most recent fiscal quarter (the registrant’s fourth fiscal quarter in the case of an annual report) that has materially affected, or is reasonably likely to materially affect, the registrant’s internal control over financial reporting; and

5. The registrant’s other certifying officer and I have disclosed, based on our most recent evaluation of internal control over financial reporting, to the registrant’s auditors and the audit committee of registrant’s board of directors (or persons performing the equivalent functions):

a) all significant deficiencies and material weaknesses in the design or operation of internal control over financial reporting which are reasonably likely to adversely affect the registrant’s ability to record, process, summarize and report financial information; and

b) any fraud, whether or not material, that involves management or other employees who have a significant role in the registrant’s internal controls over financial reporting.

Date: August 6, 2004	/s/ Lawrence W. Briscoe
	Lawrence W. Briscoe
	Chief Financial Officer

EX-32.1

Exhibit 32.1

CERTIFICATION OF CHIEF EXECUTIVE OFFICER AND CHIEF FINANCIAL OFFICER

PURSUANT TO

18 U.S.C. SECTION 1350,

AS ADOPTED PURSUANT TO

SECTION 906 OF THE SARBANES-OXLEY ACT OF 2002

I, Russell J. Howard, certify, pursuant to 18 U.S.C. Section 1350, as adopted pursuant to Section 906 of the Sarbanes-Oxley Act of 2002, that to the best of my knowledge the Quarterly Report of Maxygen, Inc. on Form 10-Q for the quarterly period ended June 30, 2004 fully complies with the requirements of Section 13(a) or 15(d) of the Securities Exchange Act of 1934 and that information contained in such Quarterly Report on Form 10-Q fairly presents in all material respects the financial condition and results of operations of Maxygen, Inc.

By:	/s/ Russell J. Howard
Name:	Russell J. Howard
Title:	Chief Executive Officer
Date:	August 6, 2004

I, Lawrence W. Briscoe, certify, pursuant to 18 U.S.C. Section 1350, as adopted pursuant to Section 906 of the Sarbanes-Oxley Act of 2002, that to the best of my knowledge the Quarterly Report of Maxygen, Inc. on Form 10-Q for the quarterly period ended June 30, 2004 fully complies with the requirements of Section 13(a) or 15(d) of the Securities Exchange Act of 1934 and that information contained in such Quarterly Report on Form 10-Q fairly presents in all material respects the financial condition and results of operations of Maxygen, Inc.

By:	/s/ Lawrence W. Briscoe
Name:	Lawrence W. Briscoe
Title:	Chief Financial Officer
Date:	August 6, 2004