Contact:

Doug Farrell

Vice President of Investor Relations

AFFYMETRIX REPORTS THIRD QUARTER 2009 RESULTS

– Company reports total revenue of $78.2 million and net loss of $8.8 million –

Santa Clara, Calif.—October 21, 2009—Affymetrix Inc., (NASDAQ: AFFX) today reported its operating results for the third quarter of 2009. Total revenue for the quarter was $78.2 million, as compared to total revenue of $75.2 million in the third quarter of 2008. In constant currency terms, the third quarter of 2009 was negatively impacted by $1.2 million as compared to the third quarter of 2008.

Product revenue was $66.2 million, which consisted of consumable revenue of $62.0 million and instrument revenue of $4.2 million.  Service revenue was $9.9 million, and royalties and other revenue were $2.1 million. This compares to third quarter 2008 product revenue of $66.0 million, service revenue of $6.1 million, and royalties and other revenue of $3.1 million.

Affymetrix shipped 21 systems in the third quarter of 2009, bringing its cumulative systems shipped to about 1,890.

The Company reported a net loss of approximately $8.8 million, or $0.13 per diluted share, in the third quarter of 2009 which included a pretax restructuring credit of $0.3 million.  This compares to a net loss of $31.8 million, or $0.46 per diluted share, in the third quarter of 2008, which included a pretax restructuring charge of $14.6 million, or $0.21 per diluted share.

Cost of product sales was $30.7 million in the third quarter of 2009 as compared to $32.3 million in the same period of 2008. Cost of services and other was $5.1 million compared to $5.8 million in the third quarter of 2008.

Product gross margin was 54 percent in the third quarter of 2009 compared to 51 percent in the third quarter of 2008.

Operating expenses were $49.1 million for the third quarter of 2009, which includes restructuring credit of $0.3 million, as compared to operating expenses of $68.8 million in the third quarter of 2008, which included restructuring charges and in-process research and development costs of $14.6 million and $5.1 million, respectively.

“Revenue for the third quarter increased 4% over the prior year and was within the range of our guidance,” stated Kevin King, CEO of Affymetrix. “While gross margin improved by 5 points over last year, we have more work to do to generate additional margin contribution from new products going forward. Finally, we maintained good control of our operating expenses.”

King continued, “I’m very excited about the launch of our Axiom Genotyping Solution, and our groundbreaking partnership with Kaiser Permanente and the University of California, San Francisco on one of the largest genotyping projects ever that will study disease, health and aging with our new platform.”

Quarterly Highlights

Genotyping

In October, Kaiser Permanente and the University of California at San Francisco (UCSF) entered into an agreement with Affymetrix to conduct genome-wide analyses of DNA samples from 100,000 Kaiser Permanente members for a large-scale research program designed to create a new resource for studying disease, health, and aging. Scientists from the program will use the just-launched Axiom Genotyping Solution, which delivers high-throughput, automated technology enabling researchers to find novel and common genetic variations associated with complex disease.

Instrumentation

Affymetrix and Beckman Coulter announced an agreement to offer researchers co-developed products from the market leaders in microarrays and automated liquid handlers. The collaboration will provide scientists with optimized, robust solutions for genomic research. This partnership will yield an expanding list of Affymetrix-validated automated target preparation methods, developed on an Affymetrix-specific configuration of Beckman Coulter’s precise and reliable Biomek FXp Liquid Handler.

Affymetrix' management team will host a conference call on October 21, 2009 at 2:00 p.m. PT to review its operating results for the third quarter of 2009. A live webcast can be accessed by visiting the Investor Relations section of the Company’s website at www.affymetrix.com. In addition, investors and other interested parties can listen by dialing domestic: (866) 500-AFFX, international: (706) 643-2771.

A replay of this call will be available from 5:00 p.m. PT on October 21, 2009 until 8:00 p.m. PT on October 28, 2009 at the following numbers: domestic: (800) 642-1687, international: (706) 645-9291. The passcode for both replays is 34032730.  An archived webcast of the conference call will be available under the Investor Relations section of the Company's website at www.affymetrix.com.

About Affymetrix

GeneChip® microarray technology is the industry-standard tool for analyzing complex genetic information. After inventing the technology in the late 1980s, Affymetrix scientists have been dedicated to developing innovative products that provide researchers with a more complete view of the genome. These products accelerate genetic research that will allow physicians to develop diagnostics and tailor treatments for individual patients by identifying and measuring the genetic information associated with complex diseases. Today, Affymetrix technology is used by the world's top pharmaceutical, diagnostic, and biotechnology companies, as well as by leading academic, government, and non-profit organizations. Affymetrix has installed almost 1,900 systems around the world and almost 20,000 peer-reviewed papers have been published using its microarray technology. Affymetrix is headquartered in Santa Clara, California. For more information about Affymetrix, please visit the company's website at www.affymetrix.com.

All statements in this press release that are not historical are "forward-looking statements" within the meaning of Section 21E of the Securities Exchange Act as amended, including statements regarding Affymetrix' "expectations," "beliefs," "hopes," "intentions," "strategies" or the like. Such statements are subject to risks and uncertainties that could cause actual results to differ materially for Affymetrix from those projected, including, but not limited to: risk relating to past and future acquisitions, including the ability of the company to successfully integrate such acquisitions into its existing business; risks of the company's ability to achieve and sustain higher levels of revenue, higher gross margins and reduced operating expenses; uncertainties relating to technological approaches, risks associated with manufacturing and product development, including risks relating to the relocation of a substantial portion of our manufacturing; personnel retention; uncertainties relating to cost and pricing of Affymetrix products; dependence on collaborative partners; uncertainties relating to sole-source suppliers; uncertainties relating to FDA and other regulatory approvals; competition; risks relating to intellectual property of others and the uncertainties of patent protection and litigation. These and other risk factors are discussed in Affymetrix' Form 10-K for the year ended December 31, 2008, and other SEC reports, including its Quarterly Reports on Form 10-Q for subsequent quarterly periods. Affymetrix expressly disclaims any obligation or undertaking to release publicly any updates or revisions to any forward-looking statements contained herein to reflect any change in Affymetrix' expectations with regard thereto or any change in events, conditions or circumstances on which any such statements are based.

PLEASE NOTE:

Affymetrix, the Affymetrix logo, GeneChip, and all other trademarks are the property of Affymetrix, Inc.

– Financial Charts to Follow –

AFFYMETRIX, INC.

CONDENSED CONSOLIDATED BALANCE SHEETS

(IN THOUSANDS)

(UNAUDITED)

	September 30,			December 31,
	2009			2008
ASSETS:				(Note 1)
Current assets:
Cash and cash equivalents	$	62,487		$	113,292
Restricted cash—short-term portion		1,683			4,402
Available-for-sale securities—short-term portion		220,818			250,970
Accounts receivable, net		56,630			62,726
Inventories		50,556			51,333
Deferred tax assets—current portion		1,867			1,077
Prepaid expenses and other current assets		12,330			15,725
Total current assets		406,371			499,525
Available-for-sale securities—long-term portion		56,009			26,900
Property and equipment, net		70,870			89,345
Acquired technology rights, net		52,412			62,569
Deferred tax assets—long-term portion		4,410			4,764
Restricted cash—long-term portion		1,109			2,175
Other assets		25,788			28,032
Total assets	$	616,969		$	713,310
LIABILITIES AND STOCKHOLDERS’ EQUITY:
Current liabilities:
Accounts payable and accrued liabilities	$	51,911		$	62,559
Deferred revenue—current portion		14,545			16,198
Total current liabilities		66,456			78,757
Deferred revenue—long-term portion		3,329			3,583
Other long-term liabilities		10,742			10,972
Convertible notes		247,201			316,341
Stockholders’ equity:
Common stock		710			703
Additional paid-in capital		728,822			721,641
Accumulated other comprehensive income (loss)		2,804			(2,296	)
Accumulated deficit		(443,095	)		(416,391	)
Total stockholders’ equity		289,241			303,657
Total liabilities and stockholders’ equity	$	616,969		$	713,310

Note 1: The condensed consolidated balance sheet at December 31, 2008 has been derived from the audited consolidated financial statements at that date included in the Company’s Form 10-K for the fiscal year ended December 31, 2008.

AFFYMETRIX, INC.

CONDENSED CONSOLIDATED STATEMENTS OF OPERATIONS

(IN THOUSANDS)

(UNAUDITED)

	Three Months Ended						Nine Months Ended
	September 30,						September 30,
	2009			2008			2009			2008
REVENUE:
Product sales	$	66,172		$	65,952		$	198,198		$	203,780
Services		9,901			6,132			33,678			23,557
Royalties and other revenue		2,118			3,105			6,430			104,338
Total revenue		78,191			75,189			238,306			331,675
COSTS AND EXPENSES:
Cost of product sales		30,728			32,347			95,047			90,581
Cost of services and other		5,142			5,820			20,299			18,241
Research and development		18,764			20,739			60,408			59,098
Selling, general and administrative		30,608			28,409			96,276			92,782
Acquired in-process technology		-			5,100			-			5,900
Restructuring charges		(296	)		14,571			1,897			29,379
Total costs and expenses		84,946			106,986			273,927			295,981
(Loss) income from operations		(6,755	)		(31,797	)		(35,621	)		35,694
Interest income and other, net		774			1,672			1,290			10,830
Interest expense		(2,430	)		(3,497	)		(8,510	)		(10,634	)
Gain from repurchase of convertible notes		-			-			17,447			-
(Loss) income before income taxes		(8,411	)		(33,622	)		(25,394	)		35,890
Income tax provision		(408	)		1,802			(1,310	)		(25,093	)
Net (loss) income	$	(8,819	)	$	(31,820	)	$	(26,704	)	$	10,797
Basic net (loss) income per common share	$	(0.13	)	$	(0.46	)	$	(0.39	)	$	0.16
Diluted net (loss) income per common share	$	(0.13	)	$	(0.46	)	$	(0.39	)	$	0.16
Shares used in computing basic net (loss) income per common share		68,799			68,582			68,569			68,542
Shares used in computing diluted net (loss) income per common share		68,799			68,582			68,569			68,650