Exhibit 12.1

Affymetrix Inc.

Ratio of Earnings to Fixed Charges

1999 - 2004

	Three months ended March 31, 2004			Year ended December 31,
				2003			2002			2001				2000				1999
Earnings:
Income (loss) before provision for income taxes	$	(974	)	$	16,848		$	(929	)	$		(32,821	)	$		(53,390	)	$		(25,504	)
Add back fixed charges:
Interest expense	6,057			17,358			19,730			19,880				18,364				2,270
Charge for unamortized bond issuance costs	3,777			1,694			—			—				—				—
Interest portion of rental expense	173			402			378			395				287				159
Total adjusted earnings	$	9,033		$		36,302	$	19,179		$		(12,546	)	$	(34,739		)	$		(23,075	)
Fixed charges:
Interest expense	6,057			17,358			19,730			19,880				18,364				2,270
Charge for unamortized bond issuance costs	3,777			1,694			—			—				—				—
Interest portion of rent expense	173			402			378			395				287				159
Total fixed charges	$	10,007		$		19,454	$	20,108		$	20,275			$	18,651			$	2,429
Ratio of earnings to fixed charges	0.90			1.87			0.95
Deficiency of earnings to fixed charges										$		32,821		$	53,390			$		25,504

	Three months ended March 31, 2004		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	$	8,302	$	33,723
Add back fixed charges:
Interest expense		359		1,380
Amortization of issuance costs		189		797
Interest portion of rental expense	173		402
Total adjusted earnings	9,033		36,302
Fixed charges:
Interest expense	$	359	$	1,380
Amortization of issuance costs		199		797
Interest portion of rental expense	179		402
Total fixed charges	$	731	$	2,576
ProForma ratio of earnings to fixed charges	12.4		14.1