Loan Agreement between Barbara A. Caulfield and Affymetrix, Inc.

Exhibit 10.65

Loan Agreement between Xxxxxxx X. Xxxxxxxxx and Affymetrix, Inc.

As part of the Employment Offer dated July 16, 2001, Affymetrix, Inc. agrees to loan Xxxxxxx X. Xxxxxxxxx $1,200,000.00 for a term of four years or to the date Xxxxxxx X. Xxxxxxxxx leaves Affymetrix, Inc., which ever comes first.  The loan term begins the day the loan is disbursed.  The rate of interest is at the IRS imputed interest rate on the first day of the term of the loan.

Xxxxxxx X. Xxxxxxxxx will begin paying accrued interest 2 years after the first day of the term of the loan.

/s/ XXXXXXX X. XXXXXXXXX		/s/ XXXXXXX X. XXXXXXXXX
Xxxxxxx X. Xxxxxxxxx		Xxxxxxx X. Xxxxxxxxx
Senior Vice President and Chief Financial Officer		EVP & General Counsel
Date:  January 7, 2004