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Davis Polk & Wardwell

1600
El Camino Road

Menlo
Park, CA 94025

(650)
752-2000

Fax
(650) 752-2111

September 1,
2005

VIA
EDGAR SUBMISSION

Peggy
A. Fisher

Donald C. Hunt

Securities and Exchange Commission

Division of Corporation Finance

100 F Street, N.E.

Washington, DC 20549

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

Dear
Ms. Fisher and Mr. Hunt:

        This
letter responds to comments of the Staff (the "Staff") of the Securities and Exchange Commission (the
"Commission") to Barbara Caulfield of Affymetrix, Inc. (the "Company") in the letter (the
"Comment Letter") regarding the above-referenced registration statement filed July 20, 2005 (the "Registration
Statement"). The Company is concurrently filing Amendment No. 1 to the Registration Statement ("Amendment No. 1")
via EDGAR for review by the Staff. As previously discussed with Peggy Fisher during a telephone call on August 17, 2005, and in addition to the changes described below, Amendment No. 1
includes information that was previously incorporated by reference from the Company's other filings with the Commission.

        Set
forth below are the Company's responses to the Staff's comments, organized as set forth in the Comment Letter. Page references in the Company's responses below correspond to the page
numbers in Amendment No. 1. In addition, we are providing to you three courtesy copies of Amendment No. 1 via courier, marked to show changes from the Registration Statement filed with
the Commission on July 20, 2005.

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.

        In response to the Staff's comment, the Company has revised the answer to this question on pages 1 and 2 and provided additional disclosure throughout
Amendment No. 1 to provide the information requested.

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.

        In response to the Staff's comment, the Company has revised the answer to this question on pages 1 and 2 and provided additional disclosure throughout
Amendment No. 1 to provide the information requested.

3.It does not appear that ParAllele shareholders are 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.

        The Company supplementally advises the Staff that, as disclosed in the Registration Statement, the exact consideration that a ParAllele shareholder will receive
will not be known until the calculation of the potential adjustment for changes in ParAllele's working capital prior to the closing. Although based on its current working capital and projections of
its closing working capital ParAllele does not expect that there will be any such adjustment, it is impossible to predict with certainty either the closing date or ParAllele's working capital as of
such date. As a result, because of these inherent uncertainties and because the merger agreement does not cap or limit the amount of the working capital adjustment, ParAllele cannot exclude the
possibility that there will be such an adjustment at the closing, and it therefore cannot state with certainty the minimum value that its shareholders will receive.

        In
response to the Staff's comment, the Company has revised the answer to this question on pages 1 and 2 and provided additional disclosure throughout Amendment No. 1,
including:

•additional
disclosure regarding the working capital adjustment and the adjustment for cash severance and loan prepayment expenses;

•a
statement that, based on its current working capital and its projections of closing working capital, ParAllele does not expect that there will be any working capital
adjustment;

•a
statement that, notwithstanding ParAllele's expectation, there may be a working capital adjustment and that there is no cap or limit to the amount of such adjustment; and

•a
sensitivity table indicating the aggregate merger consideration that ParAllele shareholders will receive and the merger consideration a ParAllele shareholder would receive
for one share of ParAllele's stock, based on the range of working capital adjustments that ParAllele and the Company reasonably expect could occur.

        The
Company supplementally advises the Staff that the disclosure throughout Amendment No. 1 regarding the value that ParAllele shareholders are expected to receive is based on an
assumed Affymetrix common stock price of $49.5510 per share, the average closing price of Affymetrix common stock during the 30 days immediately prior to the execution of the merger agreement.
Prior to mailing the proxy statement/prospectus to ParAllele shareholders, the Company will update this assumed price and the calculations of expected value that depend upon it to reflect the closing
price of Affymetrix common stock as of the most recent practicable date prior to such mailing. The Company further supplementally advises the Staff that in the event that the adjustments to the merger
consideration are materially different from the amounts shown in the sensitivity table, it will update its disclosure accordingly in advance of the ParAllele special meeting of shareholders.

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.

        The Company supplementally advises the Staff that on August 31, 2005, ParAllele and the holders of the Notes amended the terms of the Notes to provide that
if ParAllele is subject to a change of control as a result of the merger with Affymetrix, the outstanding principal amount of and all accrued interest under each Note shall automatically convert into
that number of shares of ParAllele Series B preferred stock that, when converted into the right to receive a portion of the merger consideration pursuant to the of the merger agreement, will
entitle the holder thereof to receive an amount of merger consideration with a value equal to the outstanding principal amount under this Note at such time. As a result, upon completion of the merger,
the holders of the Notes will now receive merger consideration equal only to the principal amount of the Notes—in effect, a 0% return instead of what

2

was
previously expected to be a 112% return. The amendment did not change any other terms of the Notes.

        Additionally,
on September 1, 2005, the Company and ParAllele amended the merger agreement to remove the condition to the Company's obligations to complete the merger that
required ParAllele to obtain disinterested shareholder approval of the issuance of the Notes and the waiver or exercise of preemptive rights by, or issuance of shares of ParAllele Series B
preferred stock to, certain ParAllele shareholders. This condition was replaced with a condition requiring that none of the Notes have converted into ParAllele stock prior to the closing, other than
as a result of the merger pursuant to the terms of the amended Notes. The merger agreement amendment also clarifies that ParAllele shareholders will not be obligated under the merger agreement to
indemnify Affymetrix for any losses it may suffer in connection with claims relating to the issuance of the Notes or their conversion upon the completion of the merger.

        The
economic effect of the amendment to the Notes described above is that, upon completion of the merger, the purchasers of Notes will have made an interest-free loan to
ParAllele and will not receive any value beyond the principal amount of the Notes. As a result, the Company and ParAllele have determined that it will no longer be necessary to obtain ratification of
the issuance of the Notes by ParAllele's shareholders or any waiver or exercise of preemptive rights by holders of such rights to whom Notes were not issued. Because no disinterested shareholder vote
is being sought, the shareholders will not be giving up any rights to challenge the issuance of the Notes.

        Disclosure
regarding the amendment to the Notes, the amendment to the Merger Agreement and the factors considered by the ParAllele board of directors in approving these matters has been
added to pages 79 and 81 of Amendment No. 1.

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.

        In response to the Staff's comment, the Company has revised pages 3, 33 and 61 of Amendment No. 1.

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.

        In response to the Staff's comment, the Company has revised the answer to this question on page 3 and provided additional disclosure throughout Amendment
No. 1 to provide the information requested.

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.

        In response to the Staff's comment, the Company has revised pages 3, 4 and 77 of Amendment No. 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

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 share basis and the minimum amount ParAllele's shareholders would receive after all adjustments so they can make informed voting decisions.

        In response to the Staff's comment, the Company has revised pages 2, 8 and 62 and provided additional disclosure throughout Amendment No. 1 to
clarify the alternative forms and value of consideration that ParAllele shareholders may receive. The Company's additional disclosure regarding the value to be received by ParAllele's shareholders on
a per share basis is also discussed in the response comment 3 above.

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.

        In response to the Staff's comment, the Company has revised pages 9 and 54 of Amendment No. 1 to clarify the tax consequences of the various forms
of consideration that ParAllele shareholders may receive in the merger.

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.

        In response to the Staff's comment, the Company has revised page 10 of Amendment No. 1 to specifically identify the ParAllele executive officers and
board members who have interests in the merger and to quantify the extent of those 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.

        In response to the Staff's comment, the Company has added the requested disclosure to Amendment No. 1 on pages 36 and 37. The Company also refers
the Staff to the response to comment 4 above.

12.Quantify the extent of the dilution to those shareholders who did not participate in purchasing the Notes.

        As described above in the Company's response to comment 4, on August 31, 2005, ParAllele and the holders of the Notes amended the terms of the Notes
such that the holders of the Notes will now receive merger consideration equal only to the principal amount of the Notes—in effect, a
0% return instead of what was previously expected to be a 112% return. The Company supplementally advises the Staff that this amendment eliminated any dilution to the shareholders who are not holders
of the Notes that would otherwise have resulted from the return on the Notes in excess of their principal amount. The Company has added disclosure on pages 47 and 48 of Amendment No. 1
regarding the dilution that is now expected to result from the conversion of the Notes into merger consideration equal to their principal amount.

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.

4

        As indicated above in response to comment 4, the ParAllele shareholders are no longer being asked to ratify the issuance of the Notes.

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.

        In response to the Staff's comment, the Company has added disclosure to page 34 of Amendment No. 1 and to the proxy card indicating that proxies
voting against the merger proposal will not be used to vote in favor of adjournment unless the shareholders in question affirmatively authorize them to be voted in this manner.

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.

        In response to the Staff's comment, the Company has revised the disclosure on pages 35-38 of Amendment No. 1.

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.

        In response to the Staff's comment, the Company has added the requested disclosure to Amendment No. 1 on pages 36 and 37.

17.Describe the negotiations that took place regarding arrangements for executive offic