**EXHIBIT 31.1**

**Certification**

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

1.                 Ihave reviewed this annual report on Form 10-K/A for the period endedDecember 31, 2005 of Affymetrix, Inc.;

2.                 Basedon my knowledge, this annual report does not contain any untrue statement of amaterial fact or omit to state a material fact necessary to make the statementsmade, in light of the circumstances under which such statements were made, notmisleading with respect to the period covered by this annual report;

3.                 Basedon my knowledge, the financial statements, and other financial informationincluded in this annual report, fairly present in all material respects thefinancial condition, results of operations and cash flows of the registrant asof, and for, the periods presented in this annual report;

4.                 Theregistrant’s other certifying officer and I are responsible for establishingand maintaining disclosure controls and procedures (as defined in Exchange ActRules 13a-15(e) and 15d-15(e)) and internal control overfinancial reporting (as defined in Exchange Act Rules 13a-15(f)and 15d-15(f)) for the registrant and have:

a.                  designedsuch disclosure controls and procedures, or caused such disclosure controls andprocedures to be designed under our supervision, to ensure that materialinformation relating to the registrant, including its consolidatedsubsidiaries, is made known to us by others within those entities, particularlyduring the period in which this annual report is being prepared;

b.                 designedsuch internal control over financial reporting, or caused such internal controlover financial reporting to be designed under our supervision, to providereasonable assurance regarding the reliability of financial reporting and thepreparation of financial statements for external purposes in accordance withgenerally accepted accounting principles;

c.                  evaluatedthe effectiveness of the registrant’s disclosure controls and procedures andpresented in this annual report our conclusions about the effectiveness of thedisclosure controls and procedures, as of the end of the period covered by thisannual report, based on such evaluation; and

d.                 disclosedin this annual report any change in the registrant’s internal control overfinancial reporting that occurred during the registrant’s fourth fiscal quarterthat has materially affected, or is reasonably likely to materially affect, theregistrant’s internal control over financial reporting.

5.                 Theregistrant’s other certifying officer and I have disclosed, based on our mostrecent evaluation of internal controls over financial reporting, to theregistrant’s auditors and the audit committee of the registrant’s board ofdirectors (or persons performing the equivalent functions):

a.                  allsignificant deficiencies and material weaknesses in the design or operation ofinternal controls over financial reporting which are reasonably likely toadversely affect the registrant’s ability to record, process, summarize andreport financial information; and

b.                 anyfraud, whether or not material, that involves management or other employees whohave a significant role in the registrant’s internal controls over financialreporting.
| Date: August 30, 2006 | /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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