**EXHIBIT 31.1**

**Certification of Chief Executive Officer Pursuant to Section302 of Sarbanes-Oxley Act of 2002**

I, Stephen P.A. Fodor, Ph.D., Founder, Chairman andChief Executive Officer, certify that:

1.                I have reviewed this annual report on Form 10-K/Afor the period ended December 31, 2005 of Affymetrix, Inc.;

2.                Based on my knowledge, this annualreport does not contain any untrue statement of a material fact or omit tostate a material fact necessary to make the statements made, in light of thecircumstances under which such statements were made, not misleading withrespect to the period covered by this annual report;

3.                Based on my knowledge, the financialstatements, and other financial information included in this annual report,fairly present in all material respects the financial condition, results ofoperations and cash flows of the registrant as of, and for, the periodspresented in this annual report;

4.                The registrant’s other certifyingofficer and I are responsible for establishing and maintaining disclosurecontrols and procedures (as defined in Exchange Act Rules 13a-15(e) and15d-15(e)) and internal control over financial reporting (as defined inExchange Act Rules 13a-15(f) and 15d-15(f)) for theregistrant and have:

a.                  designed such disclosure controls andprocedures, or caused such disclosure controls and procedures to be designedunder our supervision, to ensure that material information relating to theregistrant, including its consolidated subsidiaries, is made known to us byothers within those entities, particularly during the period in which thisannual report is being prepared;

b.                 designed such internal control overfinancial reporting, or caused such internal control over financial reportingto be designed under our supervision, to provide reasonable assurance regardingthe reliability of financial reporting and the preparation of financialstatements for external purposes in accordance with generally acceptedaccounting principles;

c.                  evaluated the effectiveness of theregistrant’s disclosure controls and procedures and presented in this annualreport our conclusions about the effectiveness of the disclosure controls andprocedures, as of the end of the period covered by this annual report, based onsuch evaluation; and

d.                 disclosed in this annual report anychange in the registrant’s internal control over financial reporting thatoccurred during the registrant’s fourth fiscal quarter that has materiallyaffected, or is reasonably likely to materially affect, the registrant’sinternal control over financial reporting.

5.                The registrant’s other certifyingofficer and I have disclosed, based on our most recent evaluation of internalcontrols over financial reporting, to the registrant’s auditors and the auditcommittee of the registrant’s board of directors (or persons performing theequivalent functions):

a.                  all significant deficiencies andmaterial weaknesses in the design or operation of internal controls overfinancial reporting which are reasonably likely to adversely affect theregistrant’s ability to record, process, summarize and report financialinformation; and

b.                 any fraud,whether or not material, that involves management or other employees who have asignificant role in the registrant’s internal controls over financialreporting.

| Date: July 27, 2007 | /s/ STEPHEN P.A. FODOR, PH.D |
|---------------------|------------------------------|
|                | Name:                        | Stephen P.A. Fodor, Ph.D |
|                | Title:                       | *Founder, Chairman and Chief Executive Officer* |

 

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