Exhibit 12.1

Affymetrix Inc.

Ratio of Earnings to Fixed Charges

1999 - 2003

	Year ended December 31,
	2003		2002			2001			2000			1999
Earnings:
Income (loss) before provision for income taxes	$	16,848	$	(929	)	$	(32,821	)	$	(53,390	)	$	(25,504	)
Add back fixed charges:
Interest expense	17,358		19,730			19,880			18,364			2,270
Charge for unamortized bond issuance costs	1,694		—			—			—			—
Interest portion of rental expense	402		378			395			287			159
Total adjusted earnings	36,302		19,179			(12,546		)	(34,739		)	(23,075		)
Fixed charges:
Interest expense	17,358		19,730			19,880			18,364			2,270
Charge for unamortized bond issuance costs	1,694		—			—			—			—
Interest portion of rent expense	402		378			395			287			159
Total fixed charges	19,454		20,108			20,275			18,651			2,429
Ratio of earnings to fixed charges	1.87		0.95
Deficiency of earnings to fixed charges						$	32,821		$	53,390		$	25,504

	Twelve months ended December 31, 2003
ProForma to reflect the redemption of our 2006 and 2007 Notes prior to fiscal year 2003
Earnings:
Income  before provision for income taxes	$	33,723
Add back fixed charges:
Interest expense	$	1,380
Amortization of issuance costs	$	797
Interest portion of rental expense	402
Total adjusted earnings	36,302
Fixed charges:
Interest expense	$	1,380
Amortization of issuance costs	$	797
Interest portion of rental expense	402
Total fixed charges	$	2,576
ProForma ratio of earnings to fixed charges	14.1