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    <td align="center"><FONT size=2 face="serif">As filed with the Securities and Exchange Commission
    on October 27, 2005</FONT></td>
  </tr>
  <tr>
    <td align="right"><FONT size=2 face="serif">Registration No. 333-</FONT>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</td>
  </tr>
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<P align="center"><B><FONT size=3 face="serif">SECURITIES AND EXCHANGE COMMISSION<br>
</FONT></B><FONT size=2 face="serif">Washington, D.C. 20549</FONT></P>
<hr align=center width=15% size=1 noshade color="#000000">

<P align="center"><B><FONT size=3 face="serif">FORM S-8<br>
</FONT></B><font size="3"><B><FONT face="serif">REGISTRATION STATEMENT<br>
</FONT></B></font><I><FONT size=2 face="serif">Under<br>
</FONT></I><I><FONT size=2 face="serif">The Securities Act of 1933</FONT></I></P>
<hr align=center width=15% size=1 noshade color="#000000">
<div align="center">
  <TABLE border=0 width=90% align="center" cellspacing=0 cellpadding=0>
    <TR valign="bottom">
      <TD width=33% align=center>&nbsp;</TD>
      <TD width=34% align=center>&nbsp;</TD>
      <TD width=33% align=center>&nbsp;</TD>
    </TR>
    <TR valign="bottom">
      <TD colspan=3 align=center>
    <B><FONT size=2 face="serif">AFFYMETRIX, INC.</FONT></B></TD>
    </TR>
    <TR valign="bottom">
      <TD colspan=3 align=center>
    <FONT size=2 face="serif">(Exact name of registrant as specified in its charter)</FONT>
      </TD>
    </TR>
    <TR valign="bottom">
      <TD width=33% align=center>
    <B><FONT size=2 face="serif">Delaware</FONT></B></TD>
      <TD width=34%>&nbsp;
            </TD>
      <TD width=33% align=center>
    <B><FONT size=2 face="serif">77-0319159</FONT></B></TD>
    </TR>
    <TR valign="bottom">
      <TD width=33% align=center>
    <FONT size=2 face="serif">(State or other jurisdiction</FONT></TD>
      <TD width=34%></TD>
      <TD width=33% align=center>
    <FONT size=2 face="serif">(IRS Employer Identification No.)</FONT></TD>
    </TR>
    <TR valign="bottom">
      <TD width=33% align=center>
    <FONT size=2 face="serif">of incorporation or organization)</FONT></TD>
      <TD width=34%></TD>
      <TD width=33% align=left></TD>
    </TR>
    <TR valign="bottom">
      <TD align=center></TD>
      <TD align=center></TD>
      <TD align=center></TD>
    </TR>
    <TR valign="bottom">
      <TD align=center>&nbsp;</TD>
      <TD align=center>&nbsp;</TD>
      <TD align=center>&nbsp;</TD>
    </TR>
    <TR valign="bottom">
      <TD colspan="3" align=center>
    <B><FONT size=2 face="serif">3380 CENTRAL EXPRESSWAY</FONT></B></TD>
    </TR>
    <TR valign="bottom">
      <TD colspan="3" align=center>
    <B><FONT size=2 face="serif">SANTA CLARA, CA 95051</FONT></B></TD>
    </TR>
    <TR valign="bottom">
      <TD colspan=3 align=center>
    <FONT size=2 face="serif">(Address of principal executive offices) (Zip Code)</FONT></TD>
    </TR>
    <TR valign="bottom">
      <TD colspan=3 align=center>&nbsp;</TD>
    </TR>
    <TR valign="bottom">
      <TD colspan=3 align=center><hr align=center width=15% size=1 noshade color="#000000">        </TD>
    </TR>
  </TABLE>
  <p>      <B><FONT size=2 face="serif">PARALLELE BIOSCIENCE, INC. 2001 STOCK OPTION PLAN<br>
    </FONT></B><FONT size=2 face="serif">(Full title of the Plan)</FONT></p>
  <hr align=center width=15% size=1 noshade color="#000000">
  <p><B><FONT size=2 face="serif">BARBARA A. CAULFIELD, ESQ.<br>
  </FONT></B><B><FONT size=2 face="serif">EXECUTIVE VICE PRESIDENT AND GENERAL
  COUNSEL<br>
  AFFYMETRIX, INC.<br>
  </FONT></B><B><FONT size=2 face="serif">3380 CENTRAL EXPRESSWAY<br>
  SANTA CLARA,
  CA 95051<br>
  (408) 731-5000<br>
  </FONT></B><FONT size=2 face="serif">(Name, address including zip code, and telephone number,  including area code, of agent for service)</FONT></p>
  <hr align=center width=15% size=1 noshade color="#000000">
  <p><I><FONT size=2 face="serif">Copies to:</FONT></I></p>
</div>
<P align="center">
<FONT size=2 face="serif">Martin A. Wellington, Esq.<br>
Davis Polk &amp; Wardwell<br>
1600 El Camino Real<br>
Menlo Park, California 94025<br>
(650)
752-2000</FONT></P>
 <div align="center"><B><FONT size=2 face="serif">CALCULATION OF REGISTRATION FEE</FONT></B>
 </div>
<TABLE border=1 width=100% cellspacing=2 cellpadding=2>
<TR align="center" valign="bottom">
        <TD width=28%> <font size="1"><B><FONT face="serif">Title of Securities to be Registered</FONT></B>&nbsp;
        </font></TD>
        <TD width=18%>
<B><FONT size=1 face="serif">Amount to be<br>
Registered
(1)</FONT></B></TD>
        <TD width=18%>
      <font size="1"><FONT face="serif"><strong>Proposed Maximum</strong></FONT><strong><br>
Offering
Price per Share (2)</strong></FONT>
          </TD>
        <TD width=18%>
      <font size="1"><B><FONT face="serif"> <B><FONT face="serif">Proposed Maximum<br>
Aggregate
Offering<br>
      </FONT></B> Price (2)</FONT></B>
          </font></TD>
        <TD width=18%>
      <font size="1"><B><FONT face="serif">Amount of<br>
Registration Fee(2)</FONT></B>&nbsp;
          </font></TD>
</TR>
<TR valign="bottom">
        <TD width=28% align=left>
<FONT size=2 face="serif">Common Stock, &#36;0.01 par value</FONT>&nbsp;
        </TD>
        <TD width=18% align=center>
<FONT size=2 face="serif">190,944 shares</FONT></TD>
        <TD width=18% align=center>
<FONT size=2 face="serif">&#36;43.17</FONT></TD>
        <TD width=18% align=center>
<FONT size=2 face="serif">&#36;8,243,052</FONT>
        </TD>
        <TD width=18% align=center>
<FONT size=2 face="serif">&#36;970.21</FONT></TD>
</TR>
</TABLE>
<TABLE border=0 cellspacing=0 cellpadding=0>
<TR valign="top">
        <TD width="5%" nowrap>
<FONT size=2 face="serif">(1)</FONT></TD>
        <TD width=95%>
<FONT size=2 face="serif">Pursuant to the Agreement and Plan of Merger and Reorganization dated May 31, 2005, as amended, among Registrant, Pinecone Acquisition, Inc., a wholly owned subsidiary of Affymetrix, and ParAllele BioScience, Inc, outstanding
options under the ParAllele BioScience, Inc. 2001 Stock Option Plan (as amended, the &#147;Plan&#148;) were assumed by Registrant and converted into options to purchase the Registrant&#146;s common stock. This Registration Statement shall also cover
any additional shares of common stock which become issuable under the Plan by reason of any stock dividend, stock split, recapitalization or other similar transaction effected without Registrant&#146;s receipt of consideration which results in an
increase in the number of the outstanding shares of Registrant&#146;s common stock, and the rights pursuant to the Rights Agreement dated October 15, 1998, as amended February 7, 2000.</FONT> </TD>
</TR><TR valign="top">
        <TD width="5%" nowrap>
<FONT size=2 face="serif">(2)</FONT></TD>
        <TD width=95%>
<FONT size=2 face="serif">Calculated under Rule 457(h) of the Securities Act of 1933, as amended, on the basis of the average of the high and low selling prices per share of the Registrant&#146;s Common Stock on October 21, 2005 as reported by the NASDAQ
National Market.</FONT> </TD>
</TR>
<TR valign="top"><TD colspan=2>&nbsp;</TD></TR></TABLE>

<hr size="1" noshade color="#000000" style="margin-top: -2px">
<hr size="4" noshade color="#000000" style="margin-top: -10px">
<br>
<br>
<page>
<br>
<br>

<P align="center">
<B><FONT size=2 face="serif">PART II<br>
</FONT></B><B><FONT size=2 face="serif">Information Required in the Registration Statement</FONT></B></P>
<P>
<FONT size=2 face="serif">Item 3. </FONT><U><FONT size=2 face="serif">Incorporation of Documents by Reference</FONT></U></P>
<P>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<FONT size=2 face="serif">Affymetrix, Inc. (the &#147;Registrant&#148;) hereby incorporates by reference into this Registration Statement the following documents previously filed with the Securities and Exchange Commission
(the &#147;SEC&#148;):</FONT></P>
<TABLE border=0 cellspacing=0 cellpadding=0>
<TR valign="top">
  <TD width="5%" nowrap>&nbsp;</TD>
        <TD width="5%" nowrap>
<FONT size=2 face="serif">(a)</FONT></TD>
        <TD width=90%>
<FONT size=2 face="serif">The Corporation&#146;s Annual Report on Form 10-K for the fiscal year ended December 31, 2004, filed with the SEC pursuant to Section 13 of the Securities Exchange Act of 1934, as amended (the &#147;1934 Act&#148;);</FONT>        </TD>
</TR>
<TR valign="top"><TD colspan=3>&nbsp;</TD></TR><TR valign="top">
  <TD width="5%" nowrap>&nbsp;</TD>
        <TD width="5%" nowrap>
<FONT size=2 face="serif">(b)</FONT></TD>
        <TD width=90%>
<FONT size=2 face="serif">The Corporation&#146;s Quarterly Reports on Form 10-Q for each of the fiscal quarters ended March 31, 2005 and June 30, 2005, filed with the SEC pursuant to Section 13 of the 1934 Act;</FONT>       </TD>
</TR>
<TR valign="top"><TD colspan=3>&nbsp;</TD></TR><TR valign="top">
  <TD width="5%" nowrap>&nbsp;</TD>
        <TD width="5%" nowrap>
<FONT size=2 face="serif">(c)</FONT></TD>
        <TD width=90%>
<FONT size=2 face="serif">The Corporation&#146;s Current Reports on Form 8-K
filed with the SEC on January 6, 2005, February 18, 2005, May 31, 2005 and October
26, 2005; and</FONT>     </TD>
</TR>
<TR valign="top"><TD colspan=3>&nbsp;</TD></TR><TR valign="top">
  <TD width="5%" nowrap>&nbsp;</TD>
        <TD width="5%" nowrap>
<FONT size=2 face="serif">(d)</FONT></TD>
        <TD width=90%>
<FONT size=2 face="serif">The descriptions of the Registrant&#146;s Common Stock and of certain rights associated with such Common Stock (the &#147;Rights&#148;) contained in the Registrant&#146;s registration statements on Form 8-A filed with the
Commission under Section 12 of the 1934 Act on April 16, 1996 (with respect to the Common Stock) and on October 16, 1998 and March 29, 2000 (with respect to the Rights), including any amendments or reports filed for the purpose of updating such
descriptions.</FONT>    </TD>
</TR></TABLE>
<P>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<FONT size=2 face="serif">All reports and definitive proxy or information statements filed pursuant to Section 13(a), 13(c), 14 or 15(d) of the 1934 Act after the date of this Registration Statement and prior to the filing of
a post-effective amendment which indicates that all securities offered hereby have been sold or which deregisters all securities then remaining unsold shall be deemed to be incorporated by reference into this Registration Statement and to be a part
hereof from the date of filing of such documents. Any statement contained in a document incorporated or deemed to be incorporated by reference herein shall be deemed to be modified or superseded for purposes of this Registration Statement to the
extent that a statement contained herein or in any subsequently filed document which also is deemed to be incorporated by reference herein modifies or supersedes such statement.  Any such statement so modified or superseded shall not be deemed,
except as so modified or superseded, to constitute a part of this Registration Statement.</FONT></P>
<P>
<FONT size=2 face="serif">Item 4. </FONT><U><FONT size=2 face="serif">Description of Securities</FONT></U></P>
<P>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<FONT size=2 face="serif">Not Applicable.</FONT></P>
<P>
<FONT size=2 face="serif">Item 5. </FONT><U><FONT size=2 face="serif">Interests of Named Experts and Counsel</FONT></U></P>
<P>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<FONT size=2 face="serif">Not Applicable.</FONT></P>
<P>
<FONT size=2 face="serif">Item 6. </FONT><U><FONT size=2 face="serif">Indemnification of Directors and Officers</FONT></U></P>
<P>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<FONT size=2 face="serif">Section 145 of the Delaware General Corporation Law provides that a corporation may indemnify its directors and officers as well as other employees and individuals against expenses (including
attorneys' fees), judgments, fines and amounts paid in settlement actually and reasonably incurred by such person in connection with any threatened, pending or completed actions, suits or proceedings in which such person is made a party by reason of
such person being or having been a director, officer, employee or agent to the Registrant. The Delaware General Corporation Law provides that Section 145 is not exclusive of other rights to which those seeking indemnification may be entitled under
any bylaw, agreement, vote of stockholders or disinterested directors or otherwise. Article VIII of the Registrant's bylaws provides for indemnification by the Registrant of its directors, officers and employees to the fullest extent permitted by
the Delaware General Corporation Law.</FONT></P>
<div align="center"><FONT size=2 face="serif">II-1</FONT><BR>

  <br>
  <br>
</div>
<hr size=3 color=GRAY noshade>
<page>
<br>
<br>

<P>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<FONT size=2 face="serif">Section 102(b)(7) of the Delaware General Corporation Law permits a corporation to provide in its certificate of incorporation that a director of the corporation shall not be personally liable to the
corporation or its stockholders for monetary damages for breach of fiduciary duty as a director, except for liability (i) for any breach of the director's duty of loyalty to the corporation or its stockholders, (ii) for acts or omissions not in good
faith or which involve intentional misconduct or a knowing violation of law, (iii) for unlawful payments of dividends or unlawful stock repurchases, redemptions or other distributions, or (iv) for any transaction from which the director derived an
improper personal benefit. The Registrant's certificate of incorporation provides for such limitation of liability.</FONT></P>
<P>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<FONT size=2 face="serif">The Registrant maintains standard policies of insurance under which coverage is provided (a) to its directors and officers against loss rising from claims made by reason of breach of duty or other
wrongful act, and (b) to the Registrant with respect to payments which may be made by the Registrant to such officers and directors pursuant to the above indemnification provision or otherwise as a matter of law.</FONT></P>
<P>
<FONT size=2 face="serif">Item 7. </FONT><U><FONT size=2 face="serif">Exemption from Registration Claimed</FONT></U></P>
<P>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<FONT size=2 face="serif">Not Applicable.</FONT></P>
<P>
<FONT size=2 face="serif">Item 8. </FONT><U><FONT size=2 face="serif">Exhibits</FONT></U></P>
<TABLE border=0 width=95% cellspacing=0 cellpadding=0>
<TR valign="bottom">
        <TD width=10% align=center>
<U><FONT size=2 face="serif">Exhibit Number</FONT></U></TD>
        <TD width=5% align=left>&nbsp;

        </TD>
        <TD width=85% align=left>
<U><FONT size=2 face="serif">Exhibit</FONT></U>&nbsp;
        </TD>
</TR>
<TR valign="bottom">
  <TD align=right>&nbsp;</TD>
  <TD align=left>&nbsp;</TD>
  <TD align=left>&nbsp;</TD>
</TR>
<TR valign="top">
        <TD width=10% align=right>
<FONT size=2 face="serif">4.1(1)&nbsp;&nbsp;&nbsp;</FONT>
        </TD>
        <TD width=5% align=left>&nbsp;</TD>
        <TD width=85% align=left>
<FONT size=2 face="serif">Rights Agreement, dated October 15, 1998, between Affymetrix,
Inc. and American</FONT> <FONT size=2 face="serif">Stock Transfer &amp; Trust
Company, as Rights Agent.</FONT></TD>
</TR>
<TR valign="top">
        <TD width=10% align=right>
<FONT size=2 face="serif">4.2(2)&nbsp;&nbsp;&nbsp;</FONT>
        </TD>
        <TD width=5% align=left>&nbsp;</TD>
        <TD width=85% align=left>
<FONT size=2 face="serif">Amendment No. 1 to Rights Agreement, dated as of February
7, 2000, between</FONT> <FONT size=2 face="serif">Affymetrix, Inc. and American
Stock Transfer &amp; Trust Company, as Rights Agent.</FONT> </TD>
</TR>
<TR valign="top">
        <TD width=10% align=right>
<FONT size=2 face="serif">5.1&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</FONT>
        </TD>
        <TD width=5% align=left>&nbsp;</TD>
        <TD width=85% align=left>
<FONT size=2 face="serif">Opinion of Counsel.</FONT></TD>
</TR>
<TR valign="top">
        <TD width=10% align=right>
<FONT size=2 face="serif">23.1&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</FONT>
        </TD>
        <TD width=5% align=left>&nbsp;</TD>
        <TD width=85% align=left>
<FONT size=2 face="serif">Consent of Independent Registered Public Accounting
Firm.</FONT></TD>
</TR>
<TR valign="top">
        <TD width=10% align=right>
<FONT size=2 face="serif">23.2&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</FONT>
        </TD>
        <TD width=5% align=left>&nbsp;</TD>
        <TD width=85% align=left>
<FONT size=2 face="serif">Consent of Counsel (included in Exhibit 5).</FONT></TD>
</TR>
<TR valign="top">
        <TD width=10% align=right>
<FONT size=2 face="serif">24.1&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</FONT>
        </TD>
        <TD width=5% align=left>&nbsp;</TD>
        <TD width=85% align=left>
<FONT size=2 face="serif">Powers of Attorney (included on signature page).</FONT></TD>
</TR>
<TR valign="top">
        <TD width=10% align=right>
<FONT size=2 face="serif">99.1&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</FONT>
        </TD>
        <TD width=5% align=left>&nbsp;</TD>
        <TD width=85% align=left>
<FONT size=2 face="serif">ParAllele BioScience, Inc. 2001 Stock Option Plan.</FONT></TD>
</TR>
<TR>
        <TD width="10%">
<HR noshade size=1>
        </TD>
        <TD width="5%">
<HR noshade size=1>
        </TD>
        <TD width="85%">
<HR noshade size=1>
        </TD>
</TR>
</TABLE><BR>
<TABLE width="95%" border=0 cellpadding=0 cellspacing=0>
<TR valign="top">
        <TD width="6%" nowrap>
<FONT size=2 face="serif">(1)</FONT></TD>
        <TD width=94%>
<FONT size=2 face="serif">Incorporated by reference to Exhibit 1 of the Registrant&#146;s Form 8-A as filed on October 16, 1998 (File No. 000-28218).</FONT>    </TD>
</TR>
<TR valign="top"><TD colspan=2>&nbsp;</TD></TR><TR valign="top">
        <TD width="6%" nowrap>
<FONT size=2 face="serif">(2)</FONT></TD>
        <TD width=94%>
<FONT size=2 face="serif">Incorporated by reference to Exhibit 4.1 of the Registrant&#146;s Form 8-A/A as filed on March 29, 2000 (File No. 000-28218).</FONT>  </TD>
</TR>
<TR valign="top"><TD colspan=2>&nbsp;</TD></TR></TABLE>
<P>
<FONT size=2 face="serif">Item 9. </FONT><U><FONT size=2 face="serif">Undertakings</FONT></U></P>
<P>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<FONT size=2 face="serif">A. The undersigned Registrant hereby undertakes:</FONT></P>
<blockquote>
  <p> &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<FONT size=2 face="serif">(1) to file, during any period in which offers or sales are being made, a post-effective amendment to this Registration Statement (i) to include any prospectus required by Section 10(a)(3) of the
    Securities Act of 1933 (the &#147;1933 Act&#148;), (ii) to reflect in the prospectus any facts or events arising after the effective date of this Registration Statement (or the most recent post-effective amendment thereof) which, individually or in
    the aggregate, represent a fundamental change in the information set forth in this Registration Statement and (iii) to include any material information with respect to the plan of distribution not previously disclosed in this Registration Statement
    or any material change to such information in this Registration Statement; provided, however, that clauses (1)(i) and (1)(ii) shall not apply if the information required to be included in a post-effective amendment by those paragraphs is contained
    in periodic reports filed by the Registrant pursuant to Section 13 or Section 15(d) of the 1934 Act that are incorporated by reference into this Registration Statement; </FONT></p>
</blockquote>
<div align="center"><FONT size=2 face="serif">II-2</FONT><BR>

  <br>
  <br>
</div>
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<page>
<br>
<br>

<blockquote>
  <p> &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<FONT size=2 face="serif">(2) that for the purpose of determining any liability under the 1933 Act each such post-effective amendment shall be deemed to be a new registration statement relating to the securities offered
    therein and the offering of such securities at that time shall be deemed to be the initial bona fide offering thereof; and</FONT></p>
  <p> &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<FONT size=2 face="serif">(3) to remove from registration by means of a post-effective amendment any of the securities being registered which remain unsold at the termination of the offering.</FONT></p>
</blockquote>
<P>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<FONT size=2 face="serif">B. The undersigned Registrant hereby undertakes that, for purposes of determining any liability under the 1933 Act, each filing of the Registrant&#146;s annual report pursuant to Section 13(a) or
Section 15(d) of the 1934 Act that is incorporated by reference into this Registration Statement shall be deemed to be a new registration statement relating to the securities offered therein, and the offering of such securities at that time shall be
deemed to be the initial bona fide offering thereof.</FONT></P>
<P>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<FONT size=2 face="serif">C. Insofar as indemnification for liabilities arising under the 1933 Act may be permitted to directors, officers, or controlling persons of the Registrant pursuant to the indemnification foregoing
provisions summarized in Item 6 or otherwise, the Registrant has been advised that, in the opinion of the SEC, such indemnification is against public policy as expressed in the 1933 Act, and is, therefore, unenforceable.  In the event that a claim
for indemnification against such liabilities (other than the payment by the Registrant of expenses incurred or paid by a director, officer, or controlling person of the Registrant in the successful defense of any action, suit, or proceeding) is
asserted by such director, officer, or controlling person in connection with the securities being registered, the Registrant will, unless in the opinion of its counsel the matter has been settled by controlling precedent, submit to a court of
appropriate jurisdiction the question whether such indemnification by it is against public policy as expressed in the 1933 Act and will be governed by the final adjudication of such issue.</FONT></P>
<div align="center"><FONT size=2 face="serif">II-3</FONT><BR>

  <br>
  <br>
</div>
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<page>
<br>
<br>

<P align="center">
<B><FONT size=2 face="serif">SIGNATURES</FONT></B></P>
<P>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<FONT size=2 face="serif">Pursuant to the requirements of the Securities Act of 1933, as amended, the Registrant certifies that it has reasonable grounds to believe that it meets all of the requirements for filing on Form S-8
and has duly caused this Registration Statement to be signed on its behalf by the undersigned, thereunto duly authorized, in the City of Santa Clara, State of California, on the 27th day of October, 2005.</FONT></P>
<div align="right">
  <table width="50%" border="0" cellspacing="0" cellpadding="0">
    <tr>
      <td colspan="3"> <B><FONT size=2 face="serif">AFFYMETRIX, INC.</FONT></B></td>
    </tr>
    <tr>
      <td width="7%"><font size="2" face="Times New Roman, Times, serif">&nbsp;</font></td>
      <td width="10%"><font size="2" face="Times New Roman, Times, serif">&nbsp;</font></td>
      <td width="83%"><font size="2" face="Times New Roman, Times, serif">&nbsp;</font></td>
    </tr>
    <tr>
      <td width="7%"><font size="2" face="Times New Roman, Times, serif">By:</font></td>
      <td colspan="2"><FONT size=2 face="serif">/s/ Barbara A. Caulfield</FONT></td>
    </tr>
    <tr>
      <td width="7%"><font size="2" face="Times New Roman, Times, serif">&nbsp;</font></td>
      <td colspan="2"><hr align="left" width=60% size=1 noshade color="#000000"></td>
    </tr>
    <tr>
      <td width="7%"><font size="2" face="Times New Roman, Times, serif">&nbsp;</font></td>
      <td width="10%"><font size="2" face="Times New Roman, Times, serif">Name:</font></td>
      <td width="83%"><FONT size=2 face="serif">Barbara A. Caulfield</FONT><font size="2" face="Times New Roman, Times, serif">&nbsp;</font></td>
    </tr>
    <tr>
      <td width="7%"><font size="2" face="Times New Roman, Times, serif">&nbsp;</font></td>
      <td width="10%"><font size="2" face="Times New Roman, Times, serif">Title:</font></td>
      <td width="83%"><FONT size=2 face="serif">Executive Vice President and
      General Counsel</FONT><font size="2" face="Times New Roman, Times, serif">&nbsp;</font></td>
    </tr>
  </table>
  <div align="center"><BR>
      <B><U><FONT size=2 face="serif">POWER OF ATTORNEY</FONT></U></B></div>
</div>
<P>
<B><FONT size=2 face="serif">KNOW ALL PERSONS BY THESE PRESENTS:</FONT></B></P>
<P>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<FONT size=2 face="serif">That the undersigned officers and directors of Affymetrix, Inc., a Delaware corporation, do hereby constitute and appoint Barbara A. Caulfield and Gregory T. Schiffman, and each one of them, the
lawful attorneys-in-fact and agents with full power and authority to do any and all acts and things and to execute any and all instruments which said attorneys and agents, and any one of them, determine may be necessary or advisable or required to
enable said corporation to comply with the Securities Act of 1933, as amended, and any rules or regulations or requirements of the Securities and Exchange Commission in connection with this Registration Statement. Without limiting the generality of
the foregoing power and authority, the powers granted include the power and authority to sign the names of the undersigned officers and directors in the capacities indicated below to this Registration Statement, to any and all amendments, both
pre-effective and post-effective, and supplements to this Registration Statement, and to any and all instruments or documents filed as part of or in conjunction with this Registration Statement or amendments or supplements thereof, and each of the
undersigned hereby ratifies and confirms all that said attorneys and agents, or any one of them, shall do or cause to be done by virtue hereof. This Power of Attorney may be signed in several counterparts.</FONT></P>
<P>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<B><FONT size=2 face="serif">IN WITNESS WHEREOF</FONT></B><FONT size=2 face="serif">, each of the undersigned has executed this Power of Attorney as of the date indicated.</FONT></P>
<P>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<FONT size=2 face="serif">Pursuant to the requirements of the Securities Act of 1933, as amended, this Registration Statement has been signed below by the following persons in the capacities and on the dates
indicated.</FONT></P>
<TABLE border=0 width=90% cellspacing=0 cellpadding=0>
<TR valign="bottom">
        <TD width=35% align=left>
<U><FONT size=2 face="serif">Signature</FONT></U>&nbsp;
        </TD>
        <TD width=5%>&nbsp;
        </TD>
        <TD width=35% align=left>
<U><FONT size=2 face="serif">Title</FONT></U>&nbsp;
        </TD>
        <TD width=5%>&nbsp;
        </TD>
        <TD width=20% align=left>
<U><FONT size=2 face="serif">Date</FONT></U>&nbsp;
        </TD>
</TR>
<TR valign="bottom">
  <TD align=left>&nbsp;</TD>
  <TD>&nbsp;</TD>
  <TD align=left>&nbsp;</TD>
  <TD>&nbsp;</TD>
  <TD align=left>&nbsp;</TD>
</TR>
<TR valign="bottom">
        <TD width=35% align=left>
<FONT size=2 face="serif">/s/ Stephen P.A. Fodor</FONT>&nbsp;
        </TD>
        <TD width=5%>&nbsp;
        </TD>
        <TD width=35% align=left>
<FONT size=2 face="serif">Founder, Chairman of the</FONT>&nbsp;
        </TD>
        <TD width=5%>&nbsp;
        </TD>
        <TD width=20% align=left>
<FONT size=2 face="serif">October 27, 2005</FONT>&nbsp;
        </TD>
</TR>
<TR>
        <TD width="35%">
<HR align="left" width="80%" size=1 noshade>
        </TD>
        <TD width="5%">
        </TD>
        <TD width=35% align=left valign="bottom"> <FONT size=2 face="serif">Board and
            Chief Executive</FONT>&nbsp; </TD>
        <TD width="5%">
        </TD>
        <TD width="20%">
        </TD>
</TR>
<TR valign="bottom">
        <TD width=35% align=left>
<FONT size=2 face="serif">Stephen P.A. Fodor, Ph.D.</FONT>&nbsp;
        </TD>
        <TD width=5%>&nbsp;
        </TD>
        <TD width=35% align=left> <FONT size=2 face="serif">Officer (Principal Executive</FONT>&nbsp; </TD>
        <TD width=5%>&nbsp;
        </TD>
        <TD width=20% align=left>&nbsp;

        </TD>
</TR>
<TR valign="bottom">
        <TD width=35% align=left>&nbsp;

        </TD>
        <TD width=5%>&nbsp;
        </TD>
        <TD width=35% align=left> <FONT size=2 face="serif">Officer)</FONT>&nbsp; </TD>
        <TD width=5%>&nbsp;
        </TD>
        <TD width=20% align=left>&nbsp;

        </TD>
</TR>
<TR valign="bottom">
        <TD width=35% align=left>&nbsp;

        </TD>
        <TD width=5%>&nbsp;
        </TD>
        <TD width=35% align=left>&nbsp;</TD>
        <TD width=5%>&nbsp;
        </TD>
        <TD width=20% align=left>&nbsp;

        </TD>
</TR>
<TR valign="bottom">
        <TD width=35% align=left>
<FONT size=2 face="serif">/s/ Gregory T. Schiffman</FONT>&nbsp;
        </TD>
        <TD width=5%>&nbsp;
        </TD>
        <TD width=35% align=left>
<FONT size=2 face="serif">Executive Vice President and</FONT>&nbsp;
        </TD>
        <TD width=5%>&nbsp;
        </TD>
        <TD width=20% align=left>
<FONT size=2 face="serif">October 27, 2005</FONT>&nbsp;
        </TD>
</TR>
<TR>
        <TD width="35%">
      <HR align="left" width="80%" size=1 noshade>
        </TD>
        <TD width="5%">
        </TD>
        <TD width=35% align=left valign="bottom"> <FONT size=2 face="serif">Chief Financial
            Officer</FONT>&nbsp; </TD>
        <TD width="5%">
        </TD>
        <TD width="20%">
        </TD>
</TR>
<TR valign="bottom">
        <TD width=35% align=left>
<FONT size=2 face="serif">Gregory T. Schiffman</FONT>&nbsp;
        </TD>
        <TD width=5%>&nbsp;
        </TD>
        <TD width=35% align=left> <FONT size=2 face="serif">(Principal Financial and</FONT>&nbsp; </TD>
        <TD width=5%>&nbsp;
        </TD>
        <TD width=20% align=left>&nbsp;

        </TD>
</TR>
<TR valign="bottom">
        <TD width=35% align=left>&nbsp;

        </TD>
        <TD width=5%>&nbsp;
        </TD>
        <TD width=35% align=left> <FONT size=2 face="serif">Accounting Officer)</FONT>&nbsp; </TD>
        <TD width=5%>&nbsp;
        </TD>
        <TD width=20% align=left>&nbsp;

        </TD>
</TR>
</TABLE>
<p align="center"><FONT size=2 face="serif">II-4</FONT><BR>

  <br>
  <br>
</p>
<hr size=3 color=GRAY noshade>
<page>
<br>
<br>
<br>

<TABLE border=0 width=90% cellspacing=0 cellpadding=0>
<TR valign="bottom">
        <TD width=35% align=left>
<FONT size=2 face="serif">/s/ Paul Berg</FONT>&nbsp;
        </TD>
        <TD width=5%>&nbsp;
        </TD>
        <TD width=35% align=left>&nbsp;

        </TD>
        <TD width=5%>&nbsp;
        </TD>
        <TD width=20% align=left>&nbsp;

        </TD>
</TR>
<TR>
        <TD width="35%">
      <HR align="left" width="80%" size=1 noshade>
        </TD>
        <TD width="5%">
        </TD>
        <TD width="35%">
        </TD>
        <TD width="5%">
        </TD>
        <TD width="20%">
        </TD>
</TR>
<TR valign="bottom">
        <TD width=35% align=left>
<FONT size=2 face="serif">Paul Berg, Ph. D.</FONT>&nbsp;
        </TD>
        <TD width=5%>&nbsp;
        </TD>
        <TD width=35% align=left>
<FONT size=2 face="serif">Director</FONT>&nbsp;
        </TD>
        <TD width=5%>&nbsp;
        </TD>
        <TD width=20% align=left>
<FONT size=2 face="serif">October 27, 2005</FONT>&nbsp;
        </TD>
</TR>
<TR valign="bottom">
  <TD align=left>&nbsp;</TD>
  <TD>&nbsp;</TD>
  <TD align=left>&nbsp;</TD>
  <TD>&nbsp;</TD>
  <TD align=left>&nbsp;</TD>
</TR>
<TR valign="bottom">
  <TD align=left>&nbsp;</TD>
  <TD>&nbsp;</TD>
  <TD align=left>&nbsp;</TD>
  <TD>&nbsp;</TD>
  <TD align=left>&nbsp;</TD>
</TR>
<TR valign="bottom">
        <TD width=35% align=left>
<FONT size=2 face="serif">/s/ Susan Desmond-Hellmann</FONT>&nbsp;
        </TD>
        <TD width=5%>&nbsp;
        </TD>
        <TD width=35% align=left>&nbsp;

        </TD>
        <TD width=5%>&nbsp;
        </TD>
        <TD width=20% align=left>&nbsp;

        </TD>
</TR>
<TR>
        <TD width="35%">
      <HR align="left" width="80%" size=1 noshade>
        </TD>
        <TD width="5%">
        </TD>
        <TD width="35%">
        </TD>
        <TD width="5%">
        </TD>
        <TD width="20%">
        </TD>
</TR>
<TR valign="bottom">
        <TD width=35% align=left>
<FONT size=2 face="serif">Susan Desmond-Hellmann, M.D.</FONT>&nbsp;
        </TD>
        <TD width=5%>&nbsp;
        </TD>
        <TD width=35% align=left>
<FONT size=2 face="serif">Director</FONT>&nbsp;
        </TD>
        <TD width=5%>&nbsp;
        </TD>
        <TD width=20% align=left>
<FONT size=2 face="serif">October 27, 2005</FONT>&nbsp;
        </TD>
</TR>
<TR valign="bottom">
  <TD align=left>&nbsp;</TD>
  <TD>&nbsp;</TD>
  <TD align=left>&nbsp;</TD>
  <TD>&nbsp;</TD>
  <TD align=left>&nbsp;</TD>
</TR>
<TR valign="bottom">
  <TD align=left>&nbsp;</TD>
  <TD>&nbsp;</TD>
  <TD align=left>&nbsp;</TD>
  <TD>&nbsp;</TD>
  <TD align=left>&nbsp;</TD>
</TR>
<TR valign="bottom">
        <TD width=35% align=left>
<FONT size=2 face="serif">/s/ John D. Diekman</FONT>&nbsp;
        </TD>
        <TD width=5%>&nbsp;
        </TD>
        <TD width=35% align=left>&nbsp;

        </TD>
        <TD width=5%>&nbsp;
        </TD>
        <TD width=20% align=left>&nbsp;

        </TD>
</TR>
<TR>
        <TD width="35%">
      <HR align="left" width="80%" size=1 noshade>
        </TD>
        <TD width="5%">
        </TD>
        <TD width="35%">
        </TD>
        <TD width="5%">
        </TD>
        <TD width="20%">
        </TD>
</TR>
<TR valign="bottom">
        <TD width=35% align=left>
<FONT size=2 face="serif">John D. Diekman, Ph. D.</FONT>&nbsp;
        </TD>
        <TD width=5%>&nbsp;
        </TD>
        <TD width=35% align=left>
<FONT size=2 face="serif">Director</FONT>&nbsp;
        </TD>
        <TD width=5%>&nbsp;
        </TD>
        <TD width=20% align=left>
<FONT size=2 face="serif">October 27, 2005</FONT>&nbsp;
        </TD>
</TR>
<TR valign="bottom">
  <TD align=left>&nbsp;</TD>
  <TD>&nbsp;</TD>
  <TD align=left>&nbsp;</TD>
  <TD>&nbsp;</TD>
  <TD align=left>&nbsp;</TD>
</TR>
<TR valign="bottom">
  <TD align=left>&nbsp;</TD>
  <TD>&nbsp;</TD>
  <TD align=left>&nbsp;</TD>
  <TD>&nbsp;</TD>
  <TD align=left>&nbsp;</TD>
</TR>
<TR valign="bottom">
        <TD width=35% align=left>
<FONT size=2 face="serif">/s/ Vernon R. Loucks, Jr.</FONT>&nbsp;
        </TD>
        <TD width=5%>&nbsp;
        </TD>
        <TD width=35% align=left>&nbsp;

        </TD>
        <TD width=5%>&nbsp;
        </TD>
        <TD width=20% align=left>&nbsp;

        </TD>
</TR>
<TR>
        <TD width="35%">
      <HR align="left" width="80%" size=1 noshade>
        </TD>
        <TD width="5%">
        </TD>
        <TD width="35%">
        </TD>
        <TD width="5%">
        </TD>
        <TD width="20%">
        </TD>
</TR>
<TR valign="bottom">
        <TD width=35% align=left>
<FONT size=2 face="serif">Vernon R. Loucks, Jr.</FONT>&nbsp;
        </TD>
        <TD width=5%>&nbsp;
        </TD>
        <TD width=35% align=left>
<FONT size=2 face="serif">Director</FONT>&nbsp;
        </TD>
        <TD width=5%>&nbsp;
        </TD>
        <TD width=20% align=left>
<FONT size=2 face="serif">October 27, 2005</FONT>&nbsp;
        </TD>
</TR>
<TR valign="bottom">
  <TD align=left>&nbsp;</TD>
  <TD>&nbsp;</TD>
  <TD align=left>&nbsp;</TD>
  <TD>&nbsp;</TD>
  <TD align=left>&nbsp;</TD>
</TR>
<TR valign="bottom">
  <TD align=left>&nbsp;</TD>
  <TD>&nbsp;</TD>
  <TD align=left>&nbsp;</TD>
  <TD>&nbsp;</TD>
  <TD align=left>&nbsp;</TD>
</TR>
<TR valign="bottom">
        <TD width=35% align=left>
<FONT size=2 face="serif">/s/ Susan E. Siegel</FONT>&nbsp;
        </TD>
        <TD width=5%>&nbsp;
        </TD>
        <TD width=35% align=left>&nbsp;

        </TD>
        <TD width=5%>&nbsp;
        </TD>
        <TD width=20% align=left>&nbsp;

        </TD>
</TR>
<TR>
        <TD width="35%">
      <HR align="left" width="80%" size=1 noshade>
        </TD>
        <TD width="5%">
        </TD>
        <TD width="35%">
        </TD>
        <TD width="5%">
        </TD>
        <TD width="20%">
        </TD>
</TR>
<TR valign="bottom">
        <TD width=35% align=left>
<FONT size=2 face="serif">Susan E. Siegel</FONT>&nbsp;
        </TD>
        <TD width=5%>&nbsp;
        </TD>
        <TD width=35% align=left>
<FONT size=2 face="serif">Director</FONT>&nbsp;
        </TD>
        <TD width=5%>&nbsp;
        </TD>
        <TD width=20% align=left>
<FONT size=2 face="serif">October 27, 2005</FONT>&nbsp;
        </TD>
</TR>
<TR valign="bottom">
  <TD align=left>&nbsp;</TD>
  <TD>&nbsp;</TD>
  <TD align=left>&nbsp;</TD>
  <TD>&nbsp;</TD>
  <TD align=left>&nbsp;</TD>
</TR>
<TR valign="bottom">
  <TD align=left>&nbsp;</TD>
  <TD>&nbsp;</TD>
  <TD align=left>&nbsp;</TD>
  <TD>&nbsp;</TD>
  <TD align=left>&nbsp;</TD>
</TR>
<TR valign="bottom">
        <TD width=35% align=left>
<FONT size=2 face="serif">/s/ David B. Singer</FONT>&nbsp;
        </TD>
        <TD width=5%>&nbsp;
        </TD>
        <TD width=35% align=left>&nbsp;

        </TD>
        <TD width=5%>&nbsp;
        </TD>
        <TD width=20% align=left>&nbsp;

        </TD>
</TR>
<TR>
        <TD width="35%">
      <HR align="left" width="80%" size=1 noshade>
        </TD>
        <TD width="5%">
        </TD>
        <TD width="35%">
        </TD>
        <TD width="5%">
        </TD>
        <TD width="20%">
        </TD>
</TR>
<TR valign="bottom">
        <TD width=35% align=left>
<FONT size=2 face="serif">David B. Singer</FONT>&nbsp;
        </TD>
        <TD width=5%>&nbsp;
        </TD>
        <TD width=35% align=left>
<FONT size=2 face="serif">Director</FONT>&nbsp;
        </TD>
        <TD width=5%>&nbsp;
        </TD>
        <TD width=20% align=left>
<FONT size=2 face="serif">October 27, 2005</FONT>&nbsp;
        </TD>
</TR>
<TR valign="bottom">
  <TD align=left>&nbsp;</TD>
  <TD>&nbsp;</TD>
  <TD align=left>&nbsp;</TD>
  <TD>&nbsp;</TD>
  <TD align=left>&nbsp;</TD>
</TR>
<TR valign="bottom">
  <TD align=left>&nbsp;</TD>
  <TD>&nbsp;</TD>
  <TD align=left>&nbsp;</TD>
  <TD>&nbsp;</TD>
  <TD align=left>&nbsp;</TD>
</TR>
<TR valign="bottom">
        <TD width=35% align=left>
<FONT size=2 face="serif">/s/ John A. Young</FONT>&nbsp;
        </TD>
        <TD width=5%>&nbsp;
        </TD>
        <TD width=35% align=left>&nbsp;

        </TD>
        <TD width=5%>&nbsp;
        </TD>
        <TD width=20% align=left>&nbsp;

        </TD>
</TR>
<TR>
        <TD width="35%">
      <HR align="left" width="80%" size=1 noshade>
        </TD>
        <TD width="5%">
        </TD>
        <TD width="35%">
        </TD>
        <TD width="5%">
        </TD>
        <TD width="20%">
        </TD>
</TR>
<TR valign="bottom">
        <TD width=35% align=left>
<FONT size=2 face="serif">John A. Young</FONT>&nbsp;
        </TD>
        <TD width=5%>&nbsp;
        </TD>
        <TD width=35% align=left>
<FONT size=2 face="serif">Director</FONT>&nbsp;
        </TD>
        <TD width=5%>&nbsp;
        </TD>
        <TD width=20% align=left>
<FONT size=2 face="serif">October 27, 2005</FONT>&nbsp;
        </TD>
</TR>
</TABLE><BR>
<P align="center">
<FONT size=2 face="serif">II-5</FONT></P>

<br>
<br>
<hr size=3 color=GRAY noshade>
<page>
<br>
<br>
<br>
<TABLE border=0 width=95% cellspacing=0 cellpadding=0>
  <TR valign="bottom">
    <TD colspan="3" align=center><B><FONT size=2 face="serif">EXHIBIT INDEX</FONT></B></TD>
  </TR>
  <TR valign="bottom">
    <TD align=center>&nbsp;</TD>
    <TD align=left>&nbsp;</TD>
    <TD align=left>&nbsp;</TD>
  </TR>
  <TR valign="bottom">
    <TD width=10% align=center> <U><FONT size=2 face="serif">Exhibit Number</FONT></U></TD>
    <TD width=5% align=left>&nbsp; </TD>
    <TD width=85% align=left> <U><FONT size=2 face="serif">Exhibit</FONT></U>&nbsp; </TD>
  </TR>
  <TR valign="bottom">
    <TD align=right>&nbsp;</TD>
    <TD align=left>&nbsp;</TD>
    <TD align=left>&nbsp;</TD>
  </TR>
  <TR valign="top">
    <TD width=10% align=right> <FONT size=2 face="serif">4.1(1)&nbsp;&nbsp;&nbsp;</FONT> </TD>
    <TD width=5% align=left>&nbsp;</TD>
    <TD width=85% align=left> <FONT size=2 face="serif">Rights Agreement, dated
        October 15, 1998, between Affymetrix, Inc. and American</FONT> <FONT size=2 face="serif">Stock
        Transfer &amp; Trust Company, as Rights Agent.</FONT></TD>
  </TR>
  <TR valign="top">
    <TD width=10% align=right> <FONT size=2 face="serif">4.2(2)&nbsp;&nbsp;&nbsp;</FONT> </TD>
    <TD width=5% align=left>&nbsp;</TD>
    <TD width=85% align=left> <FONT size=2 face="serif">Amendment No. 1 to Rights
        Agreement, dated as of February 7, 2000, between</FONT> <FONT size=2 face="serif">Affymetrix,
        Inc. and American Stock Transfer &amp; Trust Company, as Rights Agent.</FONT> </TD>
  </TR>
  <TR valign="top">
    <TD width=10% align=right> <FONT size=2 face="serif">5.1&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</FONT> </TD>
    <TD width=5% align=left>&nbsp;</TD>
    <TD width=85% align=left> <FONT size=2 face="serif">Opinion of Counsel.</FONT>&nbsp; </TD>
  </TR>
  <TR valign="top">
    <TD width=10% align=right> <FONT size=2 face="serif">23.1&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</FONT> </TD>
    <TD width=5% align=left>&nbsp;</TD>
    <TD width=85% align=left> <FONT size=2 face="serif">Consent of Independent
        Registered Public Accounting Firm.</FONT>&nbsp; </TD>
  </TR>
  <TR valign="top">
    <TD width=10% align=right> <FONT size=2 face="serif">23.2&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</FONT> </TD>
    <TD width=5% align=left>&nbsp;</TD>
    <TD width=85% align=left> <FONT size=2 face="serif">Consent of Counsel (included
        in Exhibit 5).</FONT>&nbsp; </TD>
  </TR>
  <TR valign="top">
    <TD width=10% align=right> <FONT size=2 face="serif">24.1&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</FONT> </TD>
    <TD width=5% align=left>&nbsp;</TD>
    <TD width=85% align=left> <FONT size=2 face="serif">Powers of Attorney (included
        on signature page).</FONT>&nbsp; </TD>
  </TR>
  <TR valign="top">
    <TD width=10% align=right> <FONT size=2 face="serif">99.1&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</FONT> </TD>
    <TD width=5% align=left>&nbsp;</TD>
    <TD width=85% align=left> <FONT size=2 face="serif">ParAllele BioScience,
        Inc. 2001 Stock Option Plan.</FONT>&nbsp; </TD>
  </TR>
  <TR>
    <TD width="10%">
      <HR noshade size=1>
    </TD>
    <TD width="5%">
      <HR noshade size=1>
    </TD>
    <TD width="85%">
      <HR noshade size=1>
    </TD>
  </TR>
</TABLE>
<BR>
<TABLE width="95%" border=0 cellpadding=0 cellspacing=0>
<TR valign="top">
        <TD width="5%" nowrap>
<FONT size=2 face="serif">(1)</FONT></TD>
        <TD width=95%>
<FONT size=2 face="serif">Incorporated by reference to Exhibit 1 of the Registrant&#146;s Form 8-A as filed on October 16, 1998 (File No. 000-28218).</FONT>    </TD>
</TR>
<TR valign="top"><TD colspan=2>&nbsp;</TD></TR><TR valign="top">
        <TD width="5%" nowrap>
<FONT size=2 face="serif">(2)</FONT></TD>
        <TD width=95%>
<FONT size=2 face="serif">Incorporated by reference to Exhibit 4.1 of the Registrant&#146;s Form 8-A/A as filed on March 29, 2000 (File No. 000-28218).</FONT>  </TD>
</TR>
<TR><TD colspan=2>&nbsp;</TD></TR></TABLE>

<br>
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<hr size=3 color=GRAY noshade>
<br>
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</BODY>
</HTML>
[{"type": "S-8", "sequence": "1", "filename": "oct2605_s8.htm", "secsgml_size_bytes": 43988}]
{"company-data": {"conformed-name": "AFFYMETRIX INC", "cik": "0000913077", "assigned-sic": "3826", "irs-number": "770319159", "state-of-incorporation": "DE", "fiscal-year-end": "1231"}, "filing-values": {"form-type": "S-8", "act": "33", "file-number": "333-129269", "film-number": "051160320"}, "business-address": {"street1": "3380 CENTRAL EXPRESSWAY", "city": "SANTA CLARA", "state": "CA", "zip": "95051", "phone": "4085226000"}, "mail-address": {"street1": "3380 CENTRAL EXPRESSWAY", "city": "SANTA CLARA", "state": "CA", "zip": "95051"}}
As filed with the Securities and Exchange Commission
    on October 27, 2005
Registration No. 333-
SECURITIES AND EXCHANGE COMMISSION
Washington, D.C. 20549
FORM S-8
REGISTRATION STATEMENT
Under
The Securities Act of 1933
AFFYMETRIX, INC.
(Exact name of registrant as specified in its charter)
Delaware
77-0319159
(State or other jurisdiction
(IRS Employer Identification No.)
of incorporation or organization)
3380 CENTRAL EXPRESSWAY
SANTA CLARA, CA 95051
(Address of principal executive offices) (Zip Code)
PARALLELE BIOSCIENCE, INC. 2001 STOCK OPTION PLAN
(Full title of the Plan)
BARBARA A. CAULFIELD, ESQ.
EXECUTIVE VICE PRESIDENT AND GENERAL
  COUNSEL
AFFYMETRIX, INC.
3380 CENTRAL EXPRESSWAY
SANTA CLARA,
  CA 95051
(408) 731-5000
(Name, address including zip code, and telephone number,  including area code, of agent for service)
Copies to:
Martin A. Wellington, Esq.
Davis Polk & Wardwell
1600 El Camino Real
Menlo Park, California 94025
(650)
752-2000
CALCULATION OF REGISTRATION FEE
Title of Securities to be Registered
Amount to be
Registered
(1)
Proposed Maximum
Offering
Price per Share (2)
Proposed Maximum
Aggregate
Offering
Price (2)
Amount of
Registration Fee(2)
Common Stock, $0.01 par value
190,944 shares
$43.17
$8,243,052
$970.21
(1)
Pursuant to the Agreement and Plan of Merger and Reorganization dated May 31, 2005, as amended, among Registrant, Pinecone Acquisition, Inc., a wholly owned subsidiary of Affymetrix, and ParAllele BioScience, Inc, outstanding
options under the ParAllele BioScience, Inc. 2001 Stock Option Plan (as amended, the "Plan") were assumed by Registrant and converted into options to purchase the Registrant's common stock. This Registration Statement shall also cover
any additional shares of common stock which become issuable under the Plan by reason of any stock dividend, stock split, recapitalization or other similar transaction effected without Registrant's receipt of consideration which results in an
increase in the number of the outstanding shares of Registrant's common stock, and the rights pursuant to the Rights Agreement dated October 15, 1998, as amended February 7, 2000.
(2)
Calculated under Rule 457(h) of the Securities Act of 1933, as amended, on the basis of the average of the high and low selling prices per share of the Registrant's Common Stock on October 21, 2005 as reported by the NASDAQ
National Market.
PART II
Information Required in the Registration Statement
Item 3.
Incorporation of Documents by Reference
Affymetrix, Inc. (the "Registrant") hereby incorporates by reference into this Registration Statement the following documents previously filed with the Securities and Exchange Commission
(the "SEC"):
(a)
The Corporation's Annual Report on Form 10-K for the fiscal year ended December 31, 2004, filed with the SEC pursuant to Section 13 of the Securities Exchange Act of 1934, as amended (the "1934 Act");
(b)
The Corporation's Quarterly Reports on Form 10-Q for each of the fiscal quarters ended March 31, 2005 and June 30, 2005, filed with the SEC pursuant to Section 13 of the 1934 Act;
(c)
The Corporation's Current Reports on Form 8-K
filed with the SEC on January 6, 2005, February 18, 2005, May 31, 2005 and October
26, 2005; and
(d)
The descriptions of the Registrant's Common Stock and of certain rights associated with such Common Stock (the "Rights") contained in the Registrant's registration statements on Form 8-A filed with the
Commission under Section 12 of the 1934 Act on April 16, 1996 (with respect to the Common Stock) and on October 16, 1998 and March 29, 2000 (with respect to the Rights), including any amendments or reports filed for the purpose of updating such
descriptions.
All reports and definitive proxy or information statements filed pursuant to Section 13(a), 13(c), 14 or 15(d) of the 1934 Act after the date of this Registration Statement and prior to the filing of
a post-effective amendment which indicates that all securities offered hereby have been sold or which deregisters all securities then remaining unsold shall be deemed to be incorporated by reference into this Registration Statement and to be a part
hereof from the date of filing of such documents. Any statement contained in a document incorporated or deemed to be incorporated by reference herein shall be deemed to be modified or superseded for purposes of this Registration Statement to the
extent that a statement contained herein or in any subsequently filed document which also is deemed to be incorporated by reference herein modifies or supersedes such statement.  Any such statement so modified or superseded shall not be deemed,
except as so modified or superseded, to constitute a part of this Registration Statement.
Item 4.
Description of Securities
Not Applicable.
Item 5.
Interests of Named Experts and Counsel
Not Applicable.
Item 6.
Indemnification of Directors and Officers
Section 145 of the Delaware General Corporation Law provides that a corporation may indemnify its directors and officers as well as other employees and individuals against expenses (including
attorneys' fees), judgments, fines and amounts paid in settlement actually and reasonably incurred by such person in connection with any threatened, pending or completed actions, suits or proceedings in which such person is made a party by reason of
such person being or having been a director, officer, employee or agent to the Registrant. The Delaware General Corporation Law provides that Section 145 is not exclusive of other rights to which those seeking indemnification may be entitled under
any bylaw, agreement, vote of stockholders or disinterested directors or otherwise. Article VIII of the Registrant's bylaws provides for indemnification by the Registrant of its directors, officers and employees to the fullest extent permitted by
the Delaware General Corporation Law.
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Section 102(b)(7) of the Delaware General Corporation Law permits a corporation to provide in its certificate of incorporation that a director of the corporation shall not be personally liable to the
corporation or its stockholders for monetary damages for breach of fiduciary duty as a director, except for liability (i) for any breach of the director's duty of loyalty to the corporation or its stockholders, (ii) for acts or omissions not in good
faith or which involve intentional misconduct or a knowing violation of law, (iii) for unlawful payments of dividends or unlawful stock repurchases, redemptions or other distributions, or (iv) for any transaction from which the director derived an
improper personal benefit. The Registrant's certificate of incorporation provides for such limitation of liability.
The Registrant maintains standard policies of insurance under which coverage is provided (a) to its directors and officers against loss rising from claims made by reason of breach of duty or other
wrongful act, and (b) to the Registrant with respect to payments which may be made by the Registrant to such officers and directors pursuant to the above indemnification provision or otherwise as a matter of law.
Item 7.
Exemption from Registration Claimed
Not Applicable.
Item 8.
Exhibits
Exhibit Number
Exhibit
4.1(1)
Rights Agreement, dated October 15, 1998, between Affymetrix,
Inc. and American
Stock Transfer & Trust
Company, as Rights Agent.
4.2(2)
Amendment No. 1 to Rights Agreement, dated as of February
7, 2000, between
Affymetrix, Inc. and American
Stock Transfer & Trust Company, as Rights Agent.
5.1
Opinion of Counsel.
23.1
Consent of Independent Registered Public Accounting
Firm.
23.2
Consent of Counsel (included in Exhibit 5).
24.1
Powers of Attorney (included on signature page).
99.1
ParAllele BioScience, Inc. 2001 Stock Option Plan.
(1)
Incorporated by reference to Exhibit 1 of the Registrant's Form 8-A as filed on October 16, 1998 (File No. 000-28218).
(2)
Incorporated by reference to Exhibit 4.1 of the Registrant's Form 8-A/A as filed on March 29, 2000 (File No. 000-28218).
Item 9.
Undertakings
A. The undersigned Registrant hereby undertakes:
(1) to file, during any period in which offers or sales are being made, a post-effective amendment to this Registration Statement (i) to include any prospectus required by Section 10(a)(3) of the
    Securities Act of 1933 (the "1933 Act"), (ii) to reflect in the prospectus any facts or events arising after the effective date of this Registration Statement (or the most recent post-effective amendment thereof) which, individually or in
    the aggregate, represent a fundamental change in the information set forth in this Registration Statement and (iii) to include any material information with respect to the plan of distribution not previously disclosed in this Registration Statement
    or any material change to such information in this Registration Statement; provided, however, that clauses (1)(i) and (1)(ii) shall not apply if the information required to be included in a post-effective amendment by those paragraphs is contained
    in periodic reports filed by the Registrant pursuant to Section 13 or Section 15(d) of the 1934 Act that are incorporated by reference into this Registration Statement;
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(2) that for the purpose of determining any liability under the 1933 Act each such post-effective amendment shall be deemed to be a new registration statement relating to the securities offered
    therein and the offering of such securities at that time shall be deemed to be the initial bona fide offering thereof; and
(3) to remove from registration by means of a post-effective amendment any of the securities being registered which remain unsold at the termination of the offering.
B. The undersigned Registrant hereby undertakes that, for purposes of determining any liability under the 1933 Act, each filing of the Registrant's annual report pursuant to Section 13(a) or
Section 15(d) of the 1934 Act that is incorporated by reference into this Registration Statement shall be deemed to be a new registration statement relating to the securities offered therein, and the offering of such securities at that time shall be
deemed to be the initial bona fide offering thereof.
C. Insofar as indemnification for liabilities arising under the 1933 Act may be permitted to directors, officers, or controlling persons of the Registrant pursuant to the indemnification foregoing
provisions summarized in Item 6 or otherwise, the Registrant has been advised that, in the opinion of the SEC, such indemnification is against public policy as expressed in the 1933 Act, and is, therefore, unenforceable.  In the event that a claim
for indemnification against such liabilities (other than the payment by the Registrant of expenses incurred or paid by a director, officer, or controlling person of the Registrant in the successful defense of any action, suit, or proceeding) is
asserted by such director, officer, or controlling person in connection with the securities being registered, the Registrant will, unless in the opinion of its counsel the matter has been settled by controlling precedent, submit to a court of
appropriate jurisdiction the question whether such indemnification by it is against public policy as expressed in the 1933 Act and will be governed by the final adjudication of such issue.
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SIGNATURES
Pursuant to the requirements of the Securities Act of 1933, as amended, the Registrant certifies that it has reasonable grounds to believe that it meets all of the requirements for filing on Form S-8
and has duly caused this Registration Statement to be signed on its behalf by the undersigned, thereunto duly authorized, in the City of Santa Clara, State of California, on the 27th day of October, 2005.
AFFYMETRIX, INC.
By:
/s/ Barbara A. Caulfield
Name:
Barbara A. Caulfield
Title:
Executive Vice President and
      General Counsel
POWER OF ATTORNEY
KNOW ALL PERSONS BY THESE PRESENTS:
That the undersigned officers and directors of Affymetrix, Inc., a Delaware corporation, do hereby constitute and appoint Barbara A. Caulfield and Gregory T. Schiffman, and each one of them, the
lawful attorneys-in-fact and agents with full power and authority to do any and all acts and things and to execute any and all instruments which said attorneys and agents, and any one of them, determine may be necessary or advisable or required to
enable said corporation to comply with the Securities Act of 1933, as amended, and any rules or regulations or requirements of the Securities and Exchange Commission in connection with this Registration Statement. Without limiting the generality of
the foregoing power and authority, the powers granted include the power and authority to sign the names of the undersigned officers and directors in the capacities indicated below to this Registration Statement, to any and all amendments, both
pre-effective and post-effective, and supplements to this Registration Statement, and to any and all instruments or documents filed as part of or in conjunction with this Registration Statement or amendments or supplements thereof, and each of the
undersigned hereby ratifies and confirms all that said attorneys and agents, or any one of them, shall do or cause to be done by virtue hereof. This Power of Attorney may be signed in several counterparts.
IN WITNESS WHEREOF
, each of the undersigned has executed this Power of Attorney as of the date indicated.
Pursuant to the requirements of the Securities Act of 1933, as amended, this Registration Statement has been signed below by the following persons in the capacities and on the dates
indicated.
Signature
Title
Date
/s/ Stephen P.A. Fodor
Founder, Chairman of the
October 27, 2005
Board and
            Chief Executive
Stephen P.A. Fodor, Ph.D.
Officer (Principal Executive
Officer)
/s/ Gregory T. Schiffman
Executive Vice President and
October 27, 2005
Chief Financial
            Officer
Gregory T. Schiffman
(Principal Financial and
Accounting Officer)
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/s/ Paul Berg
Paul Berg, Ph. D.
Director
October 27, 2005
/s/ Susan Desmond-Hellmann
Susan Desmond-Hellmann, M.D.
Director
October 27, 2005
/s/ John D. Diekman
John D. Diekman, Ph. D.
Director
October 27, 2005
/s/ Vernon R. Loucks, Jr.
Vernon R. Loucks, Jr.
Director
October 27, 2005
/s/ Susan E. Siegel
Susan E. Siegel
Director
October 27, 2005
/s/ David B. Singer
David B. Singer
Director
October 27, 2005
/s/ John A. Young
John A. Young
Director
October 27, 2005
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EXHIBIT INDEX
Exhibit Number
Exhibit
4.1(1)
Rights Agreement, dated
        October 15, 1998, between Affymetrix, Inc. and American
Stock
        Transfer & Trust Company, as Rights Agent.
4.2(2)
Amendment No. 1 to Rights
        Agreement, dated as of February 7, 2000, between
Affymetrix,
        Inc. and American Stock Transfer & Trust Company, as Rights Agent.
5.1
Opinion of Counsel.
23.1
Consent of Independent
        Registered Public Accounting Firm.
23.2
Consent of Counsel (included
        in Exhibit 5).
24.1
Powers of Attorney (included
        on signature page).
99.1
ParAllele BioScience,
        Inc. 2001 Stock Option Plan.
(1)
Incorporated by reference to Exhibit 1 of the Registrant's Form 8-A as filed on October 16, 1998 (File No. 000-28218).
(2)
Incorporated by reference to Exhibit 4.1 of the Registrant's Form 8-A/A as filed on March 29, 2000 (File No. 000-28218).