Opinion Letter – Outside Counsel – S-8 Registered Securities – Affymetrix Inc.

September 1, 2011

Affymetrix, Inc.
3420 Central Expressway
Santa Clara, CA 95051

Ladies and Gentlemen:

Affymetrix Inc., a Delaware corporation (the “Company“), is
filing with the Securities and Exchange Commission a Registration Statement on
Form S-8 (the “Registration Statement“) for the purpose of
registering under the Securities Act of 1933, as amended (the
“Securities Act“), 7,000,000 shares of its common stock, par
value $0.01 per share (the “Securities“) to be issued under the
Company’s 2011 Employee Stock Purchase Plan.

We, as your counsel, have examined such documents and such matters of fact
and law that we have deemed necessary for the purpose of rendering the opinion
expressed herein. Based on the foregoing, we advise you that, in our opinion, as
of the date hereof, the Securities have been duly authorized by all necessary
corporate action on the part of the Company and, upon issuance, delivery and
payment therefor in accordance with the applicable stock plan or agreement, the
Securities will be validly issued, fully paid and non-assessable.

We are members of the Bars of the States of New York and California and the
foregoing opinion is limited to the General Corporation Law of the State of
Delaware.

We hereby consent to the filing of this opinion as an Exhibit to the
Registration Statement. In giving this consent, we do not admit that we are in
the category of persons whose consent is required under Section 7 of the
Securities Act.