SecProbe.io

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Mail Stop 6010

	August 16, 2005

Barbara A. Caulfield, Esq.
Executive Vice President, General Counsel and Secretary
Affymetrix, Inc.
3380 Central Expressway
Santa Clara, California 95051

Re:	Affymetrix, Inc.
	Registration Statement on Form S-4 Filed July 20, 2005
      File No. 333-126718

Dear Ms. Caulfield:

      We have limited our review of your filing to those issues we
have addressed in our comments.  Where indicated, we think you
should
revise your document in response to these comments.  If you
disagree,
we will consider your explanation as to why our comment is
inapplicable or a revision is unnecessary.  Please be as detailed
as
necessary in your explanation.  In some of our comments, we may
ask
you to provide us with information so we may better understand
your
disclosure.  After reviewing this information, we may raise
additional comments.

      Please understand that the purpose of our review process is
to
assist you in your compliance with the applicable disclosure
requirements and to enhance the overall disclosure in your filing.
We look forward to working with you in these respects.  We welcome
any questions you may have about our comments or any other aspect
of
our review.  Feel free to call us at the telephone numbers listed
at
the end of this letter.

What will ParAllele shareholders be entitled to receive . . .,
page 1

1. Disclose on a per share basis the amount of merger
consideration
ParAllele shareholders will receive in the merger.

2. Please revise to describe briefly the working capital and other
adjustments, and indicate the estimated amount of these
adjustments
as of a recent date.
3. It does not appear that ParAllele shareholders are not given
sufficient information to make an informed voting decision
regarding
the amount of consideration they will ultimately receive because
the
value can be adjusted downward by some unspecified amount.  If you
cannot provide more specific information regarding the value of
the
consideration, expand to state the minimum value they could
receive
so they can decide whether or not they want to vote to approve the
merger based on that amount.

Why am I being asked to ratify the issuance of the Notes?
4.  Expand the answer to state that the Notes, which were issued
during the merger negotiations with Affymetrix, were issued with
very
favorable conversion terms that permit the holders to convert at
the
time of this merger and realize a profit of 112%, or $________.
If
shareholders will be giving up any rights to challenge the initial
issuance of the Notes by ratifying them now, expand to so state.

What votes of the ParAllele shareholders are required . . .?, page
2

5. State, if true, that because ParAllele`s directors, executive
officers and shareholders affiliated with certain directors have
agreed to vote in favor of the merger, approval of that proposal
is
assured.

What is the escrow account and how does it work?, page 2

6. Please revise here and throughout the filing to quantify the
estimated dollar amount of the 9.36% merger consideration to be
placed in escrow, and disclose how this amount was determined.

Who is the shareholders` representative?, page 2

7. Disclose the decisions regarding the escrow fund that Dr.
MacQuitty will be empowered to make as a result of the approval of
Proposal 1.

What ParAllele Shareholders Will Receive, page 6

8. Revise to present the alternative forms of consideration more
clearly based on the various trading prices of Affymetrix shares,
perhaps by tabular format.  Provide the value to be received on a
per
share basis and the minimum amount ParAllele`s shareholders would
receive after all adjustments so they can make informed voting
decisions.

Material Federal Income Tax Consequences, page 7

9. While you are clear about the tax consequences if the merger
consideration consists solely of cash, you should revise the
disclosure to clarify what the tax consequences will be if
shareholders receive stock or cash and stock, rather than stating
what you "expect" the consequences to be.

Interests of ParAllele`s Officers and Directors in the Merger,
page 7

10. Please revise to identify the ParAllele executive officers and
board members who have "interests" in the merger.  Also quantify
the
extent of all interests.

Proposal 2:  The Notes, page 10
11. Expand to explain why the Board agreed to such favorable
conversion terms in the event of a change of control when it was
actively negotiating a merger at the time.  Explain how the
various
members of the Board (both those who were interested parties and
those who were not interested parties) believed that agreeing to
these terms was consistent with their fiduciary duties to
unaffiliated shareholders.
12. Quantify the extent of the dilution to those shareholders who
did
not participate in purchasing the Notes.
13. Explain why shareholders are being asked to ratify this
issuance,
what happens if they do not ratify it, and why the board
recommends
that they vote FOR the ratification.

Other Business; Adjournments, page 32

14. We note your disclosure that proxies may be used to vote to
adjourn the ParAllele special meeting in order to solicit
additional
proxies.  Revise to clarify that proxies voting against a proposal
will not be used to vote in favor of adjournment in order to
solicit
additional votes for a proposal.  If you choose to do so, you can
include a separate proposal regarding adjournment on the proxy
card.

Proposal 1 - The Merger and Related Transactions, page 32

Background of the Merger, page 32

15. Please expand your disclosure with regard to possible
strategic
relationships, business combinations and financing transactions
ParAllele considered as alternatives to the proposed merger.
Identify the alternatives and explain why they were rejected in
favor
of the proposed merger.

16. We note your disclosure on page 32 that the ParAllele board
formed an advisory committee that included Mr. Ericson, Dr.
MacQuitty
and Ms. Samuels to consider, among other things, potential equity
financing opportunities for ParAllele.  Please disclose whether in
voting to approve the convertible note financing, the ParAllele
board
considered the interests of these members of the advisory
committee
in such a transaction.  Also disclose what other financing
opportunities were considered and rejected.

17. Describe the negotiations that took place regarding
arrangements
for executive officers of ParAllele to receive employment,
severance
or other forms of compensation in addition to the per share
amounts
to be received by all existing security holders.  Explain how the
negotiations regarding these arrangements affected the
negotiations
regarding the exchange ratio.

Reasons for the Merger, page 35

18. Please disclose the identity of and services provided by the
"strategic consultant" identified on page 33.  Disclose whether
ParAllele considered the advice of the strategic consultant in
determining whether to recommend that ParAllele shareholders vote
in
favor of the merger.

19. We note there is no discussion about whether ParAllele
received a
fairness opinion.  If none was obtained, fully describe how the
ParAllele board determined that the proposed merger consideration
is
fair.  We may have further comments.

Executive Officer Severance Agreements and Employment of Certain
ParAllele Executive Officers by Affymetrix . . ., page 41

20. Please disclose all material terms of the agreements
referenced
in these sections.  For example, disclose the nature of the
consulting services to be provided by Dr. Naclerio and the fees
payable to him under this agreement.

21. Please revise your disclosure to quantify the benefits to be
received under each of the agreements described in this section.
For
example, disclose the number of shares of restricted stock held by
Dr. Naclerio that were subject to accelerated vesting.  Disclose
the
value of the shares of Affymetrix common stock that Affymetrix
recommends issuing to Dr. Krodel and Dr. Willis.

Convertible Promissory Notes, page 42

22. Please disclose all material terms of the convertible
promissory
notes, including the conversion rate, and file a form of the note
as
an annex to the proxy statement/prospectus.  Please also disclose
any
material changes to other agreements made in connection with this
issuance of the convertible notes.  We note, for example,
references
to amendments to the Series B put option in third full paragraph
on
page F-20.

Security Ownership of Management and Certain Beneficial Owners of
ParAllele, page 44

23. Identify the natural persons who beneficially own the shares
held
by Abingworth Management Limited, Index Ventures, and Versant
Ventures.

Material U.S. Federal Income Tax Consequences, page 46

24. Please revise the second paragraph on page 48 to remove the
qualification and to clarify that counsel for each of the parties
has
opined that  the merger will constitute a reorganization within
the
meaning of Section 368(a) of the Internal Revenue Code.

The Merger Agreement, page 54
Calculation of Merger Consideration, page 55

25. Disclose the circumstances under which ParAllele would elect
for
the merger consideration to be paid exclusively in cash if
Affymetrix`s average stock price during the 30 days prior to
closing
is greater than $64.4163.

Impact of the Notes on ParAllele Shareholders, page 75

26. Please describe and quantify to the extent practicable claims
arising from the issuance of the convertible notes.

Annex A

27. We note your statement that "Such information can be found
elsewhere in this proxy statement/prospectus and in the other
public
filings Affymetrix makes with the Securities and Exchange
Commission."  Please revise to remove any potential implication
that
the referenced merger agreement does not constitute public
disclosure
under the federal securities laws.

28. We note your statement that "information concerning the
subject
matter of the representations and warranties may have changed
since
the date of the agreement, which subsequent information may or may
not be fully reflected in Affymetrix`s public disclosures."
Please
be advised that, notwithstanding the inclusion of a general
disclaimer, you are responsible for considering whether additional
specific disclosures of material information regarding material
contractual provisions are required to make the statements
included
in the proxy statement/prospectus not misleading.

*  *  *  *  *

      As appropriate, please amend your registration statement in
response to these comments.  You may wish to provide us with
marked
copies of the amendment to expedite our review.  Please furnish a
cover letter with your amendment that keys your responses to our
comments and provides any requested supplemental information.
Detailed cover letters greatly facilitate our review.  Please
understand that we may have additional comments after reviewing
your
amendment and responses to our comments.

      We urge all persons who are responsible for the accuracy and
adequacy of the disclosure in the filings reviewed by the staff to
be
certain that they have provided all information investors require
for
an informed decision.  Since the company and its management are in
possession of all facts relating to a company`s disclosure, they
are
responsible for the accuracy and adequacy of the disclosures they
have made.

	Notwithstanding our comments, in the event the company
requests
acceleration of the effective date of the pending registration
statement, it should furnish a letter, at the time of such
request,
acknowledging that:

* should the Commission or the staff, acting pursuant to delegated
authority, declare the filing effective, it does not foreclose the
Commission from taking any action with respect to the filing;

* the action of the Commission or the staff, acting pursuant to
delegated authority, in declaring the filing effective, does not
relieve the company from its full responsibility for the adequacy
and
accuracy of the disclosure in the filing; and

* the company may not assert staff comments and the declaration of
effectiveness as a defense in any proceeding initiated by the
Commission or any person under the federal securities laws of the
United States.

	In addition, please be advised that the Division of
Enforcement
has access to all information you provide to the staff of the
Division of Corporation Finance in connection with our review of
your
filing or in response to our comments on your filing.

      We will consider a written request for acceleration of the
effective date of the registration statement as a confirmation of
the
fact that those requesting acceleration are aware of their
respective
responsibilities under the Securities Act of 1933 and the
Securities
Exchange Act of 1934 as they relate to the proposed public
offering
of the securities specified in the above registration statement.
We
will act on the request and, pursuant to delegated authority,
grant
acceleration of the effective date.

      We direct your attention to Rules 460 and 461 regarding
requesting acceleration of a registration statement.  Please allow
adequate time after the filing of any amendment for further review
before submitting a request for acceleration.  Please provide this
request at least two business days in advance of the requested
effective date.

      Please contact Donald C. Hunt at (202) 551-3647 or me at
(202)
551-3800 with any questions.

Sincerely,

	Peggy A. Fisher
	Assistant Director

cc (via fax):	Martin Wellington, Esq. or Mischa Travers, Esq. -
Davis Polk & Wardwell LLP
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Barbara A. Caulfield, Esq.
Affymetrix, Inc.
August 16, 2005
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