Affymetrix Inc (AFFX) SEC Filing 10-K Annual report for the fiscal year ending Sunday, December 31, 2006

EXHIBIT 99.1

FOR IMMEDIATE RELEASE

Contact:
Doug Farrell
Vice President of Investor Relations
408-731-5285

AFFYMETRIX REPORTS FOURTH QUARTER AND FISCAL YEAR 2006 RESULTS

Santa Clara, Calif. — February 7, 2007

— Affymetrix Inc., (Nasdaq: AFFX) today reported its operating results for the fourth quarter and fiscal year ended December 31, 2006.  On a GAAP basis, the Company reported net income of approximately $8.7 million or $0.13 per diluted share in the fourth quarter of 2006 as compared to net income of $30.6 million or $0.43 per diluted share in the fourth quarter of 2005.

On a GAAP basis, the Company reported fiscal year 2006 net loss of $13.7 million or $0.20 per diluted share, as compared to net income of $65.8 million or $0.96 per diluted share for 2005.

On January 1, 2006, the Company adopted FAS 123R and is reporting employee stock-based compensation expense in its GAAP results. Excluding the impact of FAS 123R, the Company reported non-GAAP net income of approximately $10.4 million or $0.15 per diluted share in the fourth quarter of 2006, and for fiscal year 2006, net loss of $2.6 million or $0.04 per diluted share.

Total revenue for the fourth quarter was $104.2 million, of which $2.6 million was related to the sale of products to Perlegen Sciences Inc., as compared to total revenue of $111.5 million in the fourth quarter of 2005, of which $2.8 million was related to the sale of products to Perlegen.  For the full year, total revenue was $355.3 million as compared to $367.6 million for 2005.

Product and product related revenue was $95.0 million for the fourth quarter of 2006, compared to $105.7 million in the same period in 2005.  Fourth quarter sales included GeneChip® consumable revenue of $72.1 million, consisting of array revenue of $49.6 million, reagent revenue of $13.0 million, genotyping services revenue of $6.9 million and $2.6 million of Perlegen revenue. Additionally, the Company reported instrument revenue of $15.0 million in the fourth quarter of 2006.

In 2006, total product and product related revenue was $323.8 million as compared to $350.2 million in 2005.  For the year, consumable revenue was $251.2 million, in-line with fiscal year 2005.  Affymetrix shipped approximately 170 systems in 2006, bringing our cumulative systems shipped to around 1550 at the end of the fourth quarter.

Royalties and other revenue were $6.6 million for the fourth quarter of 2006 compared to $3.1 million in the fourth quarter of 2005.  In 2006, royalties and other revenue increased to $16.8 million compared to $8.3 million in 2005.