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  <H5 align="left" style="page-break-before:always"><A HREF="#toc">Table of Contents</A></H5><P>
  <DIV style="font-family: 'Times New Roman',Times,serif">
  
  
  
  
  <DIV style="width: 100%; border-bottom: 2pt solid black; font-size: 1pt">&nbsp;</DIV>
  <DIV style="width: 100%; border-bottom: 1pt solid black; font-size: 1pt">&nbsp;</DIV>
  
  
  
  
  
  
  
  <DIV align="center" style="font-size: 10pt; margin-top: 18pt">As filed with the Securities and Exchange Commission on November&nbsp;15, 2005
  </DIV>
  
  
  <DIV align="right" style="font-size: 10pt; margin-top: 12pt"><B>Registration No.&nbsp;333-____________</B>
  </DIV>
  
  <DIV align="center" style="font-size: 14pt; margin-top: 12pt"><B>SECURITIES AND EXCHANGE COMMISSION</B>
  </DIV>
  
  <DIV align="center" style="font-size: 12pt"><B>WASHINGTON, D.C. 20549</B>
  </DIV>
  
  <DIV align="center"><DIV style="font-size: 3pt; margin-top: 16pt; width: 26%; border-top: 1px solid #000000">&nbsp;</DIV></DIV>
  
  <DIV align="center" style="font-size: 18pt; margin-top: 12pt"><B>FORM S-8</B>
  </DIV>
  
  
  <DIV align="center" style="font-size: 12pt; margin-top: 12pt"><B>REGISTRATION STATEMENT<BR>
  UNDER<BR>
  THE SECURITIES ACT OF 1933</B>
  </DIV>
  
  <DIV align="center" style="font-size: 24pt; margin-top: 12pt"><B>BROOKS AUTOMATION, INC.</B>
  </DIV>
  
  <DIV align="center"><DIV style="font-size: 3pt; margin-top: 1pt; width: 100%; border-top: 1px solid #000000">&nbsp;</DIV></DIV>
  
  <DIV align="center" style="font-size: 10pt">(Exact Name of Registrant as Specified in its Charter)</DIV>
  
  
  
  <DIV align="center" style="font-size: 10pt; margin-top: 18pt">Delaware
  </DIV>
  
  <DIV align="center"><DIV style="font-size: 3pt; margin-top: 1pt; width: 100%; border-top: 1px solid #000000">&nbsp;</DIV></DIV>
  
  <DIV align="center" style="font-size: 10pt">(State or Other Jurisdiction of Incorporation or Organization)</DIV>
  
  
  
  <DIV align="center" style="font-size: 10pt; margin-top: 18pt">04-3040660
  </DIV>
  
  <DIV align="center"><DIV style="font-size: 3pt; margin-top: 1pt; width: 100%; border-top: 1px solid #000000">&nbsp;</DIV></DIV>
  
  <DIV align="center" style="font-size: 10pt">(I.R.S. Employer Identification Number)</DIV>
  
  
  
  <DIV align="center" style="font-size: 10pt; margin-top: 18pt">15 Elizabeth Drive, Chelmsford, MA 01824
  </DIV>
  
  <DIV align="center"><DIV style="font-size: 3pt; margin-top: 1pt; width: 100%; border-top: 1px solid #000000">&nbsp;</DIV></DIV>
  
  <DIV align="center" style="font-size: 10pt">(Address of Principal Executive Offices)</DIV>
  
  
  
  <DIV align="center" style="font-size: 10pt; margin-top: 18pt">Helix Technology Corporation 1996 Equity Incentive Plan<BR>
  Helix Technology Corporation Amended and Restated Stock Option Plan for Non-Employee Directors<BR>
  Helix Technology Corporation 1981 Employee Stock Option Plan, as Amended
  </DIV>
  
  <DIV align="center"><DIV style="font-size: 3pt; margin-top: 1pt; width: 100%; border-top: 1px solid #000000">&nbsp;</DIV></DIV>
  
  <DIV align="center" style="font-size: 10pt">(Full Title of the Plans)</DIV>
  
  
  
  <DIV align="center" style="font-size: 10pt; margin-top: 18pt">Thomas S. Grilk<BR>
  Senior Vice President, General Counsel and Secretary<BR>
  Brooks Automation, Inc.<BR>
  15 Elizabeth Drive<BR>
  Chelmsford, MA 01824
  </DIV>
  
  <DIV align="center"><DIV style="font-size: 3pt; margin-top: 1pt; width: 100%; border-top: 1px solid #000000">&nbsp;</DIV></DIV>
  
  <DIV align="center" style="font-size: 10pt">(Name and Address of Agent for Service)</DIV>
  
  
  
  <DIV align="center" style="font-size: 10pt; margin-top: 18pt">(978)&nbsp;721-3371
  </DIV>
  
  <DIV align="center"><DIV style="font-size: 3pt; margin-top: 1pt; width: 100%; border-top: 1px solid #000000">&nbsp;</DIV></DIV>
  
  <DIV align="center" style="font-size: 10pt">(Telephone Number, Including Area Code for Agent for Service)</DIV>
  
  
  
  <DIV align="center" style="font-size: 10pt; margin-top: 18pt"><B>CALCULATION OF REGISTRATION FEE</B>
  </DIV>
  
  <DIV align="center">
  <TABLE style="font-size: 10pt" cellspacing="0" border="0" cellpadding="0" width="100%">
  <!-- Begin Table Head -->
  <TR valign="bottom">
      <TD width="1%">&nbsp;</TD>
      <TD width="54%">&nbsp;</TD>
      <TD width="2%">&nbsp;</TD><!-- VRule -->
      <TD width="2%">&nbsp;</TD>
      <TD width="1%">&nbsp;</TD>
      <TD width="5%">&nbsp;</TD>
      <TD width="1%">&nbsp;</TD>
      <TD width="2%">&nbsp;</TD><!-- VRule -->
      <TD width="2%">&nbsp;</TD>
      <TD width="1%">&nbsp;</TD>
      <TD width="5%">&nbsp;</TD>
      <TD width="1%">&nbsp;</TD>
      <TD width="2%">&nbsp;</TD><!-- VRule -->
      <TD width="2%">&nbsp;</TD>
      <TD width="1%">&nbsp;</TD>
      <TD width="5%">&nbsp;</TD>
      <TD width="1%">&nbsp;</TD>
      <TD width="2%">&nbsp;</TD><!-- VRule -->
      <TD width="2%">&nbsp;</TD>
      <TD width="1%">&nbsp;</TD>
      <TD width="5%">&nbsp;</TD>
      <TD width="1%">&nbsp;</TD>
  
      <TD width="1%">&nbsp;</TD>
  </TR><TR style="font-size: 1px" valign="bottom">
      <TD nowrap align="left" colspan="23" style="border-bottom: 3px solid #000000">&nbsp;</TD>
  </TR>
  <TR style="font-size: 8pt" valign="bottom">    <TD width="1%">&nbsp;</TD>
  
      <TD>&nbsp;</TD>
      <TD style="border-right: 2px solid #000000">&nbsp;</TD>
      <TD>&nbsp;</TD>
      <TD>&nbsp;</TD>
      <TD>&nbsp;</TD>
      <TD>&nbsp;</TD>
      <TD style="border-right: 2px solid #000000">&nbsp;</TD>
      <TD>&nbsp;</TD>
      <TD nowrap align="center" colspan="3">Proposed Maximum</TD>
      <TD style="border-right: 2px solid #000000">&nbsp;</TD>
      <TD>&nbsp;</TD>
      <TD nowrap align="center" colspan="3">Proposed</TD>
      <TD style="border-right: 2px solid #000000">&nbsp;</TD>
      <TD>&nbsp;</TD>
      <TD nowrap align="center" colspan="3">Amount of</TD>
      <TD width="1%">&nbsp;</TD>
  </TR>
  <TR style="font-size: 8pt" valign="bottom">    <TD width="1%">&nbsp;</TD>
  
      <TD nowrap align="center">Title of Securities to be</TD>
      <TD style="border-right: 2px solid #000000">&nbsp;</TD>
      <TD>&nbsp;</TD>
      <TD nowrap align="center" colspan="3">Amount to be</TD>
      <TD style="border-right: 2px solid #000000">&nbsp;</TD>
      <TD>&nbsp;</TD>
      <TD nowrap align="center" colspan="3">Offering Price Per</TD>
      <TD style="border-right: 2px solid #000000">&nbsp;</TD>
      <TD>&nbsp;</TD>
      <TD nowrap align="center" colspan="3">Maximum Aggregate</TD>
      <TD style="border-right: 2px solid #000000">&nbsp;</TD>
      <TD>&nbsp;</TD>
      <TD nowrap align="center" colspan="3">Registration</TD>
      <TD width="1%">&nbsp;</TD>
  </TR>
  <TR style="font-size: 8pt" valign="bottom">    <TD width="1%">&nbsp;</TD>
  
      <TD nowrap align="center">Registered</TD>
      <TD style="border-right: 2px solid #000000">&nbsp;</TD>
      <TD>&nbsp;</TD>
      <TD nowrap align="center" colspan="3">Registered (1)</TD>
      <TD style="border-right: 2px solid #000000">&nbsp;</TD>
      <TD>&nbsp;</TD>
      <TD nowrap align="center" colspan="3">Share (2)</TD>
      <TD style="border-right: 2px solid #000000">&nbsp;</TD>
      <TD>&nbsp;</TD>
      <TD nowrap align="center" colspan="3">Offering Price (2)</TD>
      <TD style="border-right: 2px solid #000000">&nbsp;</TD>
      <TD>&nbsp;</TD>
      <TD nowrap align="center" colspan="3">Fee (2)</TD>
      <TD width="1%">&nbsp;</TD>
  </TR>
  
  <!-- End Table Head -->
  <!-- Begin Table Body -->
  <TR valign="bottom">
      <TD width="1%" style="border-top: 2px solid #000000">&nbsp;</TD>
                      <TD style="border-top: 2px solid #000000"><DIV style="margin-left:0px; text-indent:-0px">Helix Technology
  Corporation 1996 Equity
  Incentive Plan</DIV></TD>
      <TD style="border-right: 2px solid #000000; border-top: 2px solid #000000">&nbsp;</TD>
      <TD style="border-top: 2px solid #000000">&nbsp;</TD>
      <TD style="border-top: 2px solid #000000">&nbsp;</TD>
      <TD align="right" style="border-top: 2px solid #000000">721,080</TD>
      <TD style="border-top: 2px solid #000000">&nbsp;</TD>
      <TD style="border-right: 2px solid #000000; border-top: 2px solid #000000">&nbsp;</TD>
      <TD style="border-top: 2px solid #000000">&nbsp;</TD>
      <TD align="right" style="border-top: 2px solid #000000">$</TD>
      <TD align="right" style="border-top: 2px solid #000000">13.095</TD>
      <TD style="border-top: 2px solid #000000">&nbsp;</TD>
      <TD style="border-right: 2px solid #000000; border-top: 2px solid #000000">&nbsp;</TD>
      <TD style="border-top: 2px solid #000000">&nbsp;</TD>
      <TD align="right" style="border-top: 2px solid #000000">$</TD>
      <TD align="right" style="border-top: 2px solid #000000">9,442,542.60</TD>
      <TD style="border-top: 2px solid #000000">&nbsp;</TD>
      <TD style="border-right: 2px solid #000000; border-top: 2px solid #000000">&nbsp;</TD>
      <TD style="border-top: 2px solid #000000">&nbsp;</TD>
      <TD align="right" style="border-top: 2px solid #000000">$</TD>
      <TD align="right" style="border-top: 2px solid #000000">1,111.39</TD>
      <TD style="border-top: 2px solid #000000">&nbsp;</TD>
      <TD width="1%" style="border-top: 2px solid #000000">&nbsp;</TD>
  </TR>
  <TR valign="bottom">
      <TD width="1%" style="border-top: 2px solid #000000">&nbsp;</TD>
      <TD style="border-top: 2px solid #000000"><DIV style="margin-left:0px; text-indent:-0px">Helix Technology
  Corporation Amended and
  Restated Stock Option
  Plan for Non-Employee
  Directors</DIV></TD>
      <TD style="border-right: 2px solid #000000; border-top: 2px solid #000000">&nbsp;</TD>
      <TD style="border-top: 2px solid #000000">&nbsp;</TD>
      <TD style="border-top: 2px solid #000000">&nbsp;</TD>
      <TD align="right" style="border-top: 2px solid #000000">26,640</TD>
      <TD style="border-top: 2px solid #000000">&nbsp;</TD>
      <TD style="border-right: 2px solid #000000; border-top: 2px solid #000000">&nbsp;</TD>
      <TD style="border-top: 2px solid #000000">&nbsp;</TD>
      <TD align="right" style="border-top: 2px solid #000000">$</TD>
      <TD align="right" style="border-top: 2px solid #000000">13.095</TD>
      <TD style="border-top: 2px solid #000000">&nbsp;</TD>
      <TD style="border-right: 2px solid #000000; border-top: 2px solid #000000">&nbsp;</TD>
      <TD style="border-top: 2px solid #000000">&nbsp;</TD>
      <TD align="right" style="border-top: 2px solid #000000">$</TD>
      <TD align="right" style="border-top: 2px solid #000000">348,850.80</TD>
      <TD style="border-top: 2px solid #000000">&nbsp;</TD>
      <TD style="border-right: 2px solid #000000; border-top: 2px solid #000000">&nbsp;</TD>
      <TD style="border-top: 2px solid #000000">&nbsp;</TD>
      <TD align="right" style="border-top: 2px solid #000000">$</TD>
      <TD align="right" style="border-top: 2px solid #000000">41.06</TD>
      <TD style="border-top: 2px solid #000000">&nbsp;</TD>
      <TD width="1%" style="border-top: 2px solid #000000">&nbsp;</TD>
  </TR>
  <TR valign="bottom">
      <TD width="1%" style="border-top: 2px solid #000000">&nbsp;</TD>
      <TD style="border-top: 2px solid #000000"><DIV style="margin-left:0px; text-indent:-0px">Helix Technology
  Corporation 1981
  Employee Stock Option
  Plan, as Amended</DIV></TD>
      <TD style="border-right: 2px solid #000000; border-top: 2px solid #000000">&nbsp;</TD>
      <TD style="border-top: 2px solid #000000">&nbsp;</TD>
      <TD style="border-top: 2px solid #000000">&nbsp;</TD>
      <TD align="right" style="border-top: 2px solid #000000">22,200</TD>
      <TD style="border-top: 2px solid #000000">&nbsp;</TD>
      <TD style="border-right: 2px solid #000000; border-top: 2px solid #000000">&nbsp;</TD>
      <TD style="border-top: 2px solid #000000">&nbsp;</TD>
      <TD align="right" style="border-top: 2px solid #000000">$</TD>
      <TD align="right" style="border-top: 2px solid #000000">13.095</TD>
      <TD style="border-top: 2px solid #000000">&nbsp;</TD>
      <TD style="border-right: 2px solid #000000; border-top: 2px solid #000000">&nbsp;</TD>
      <TD style="border-top: 2px solid #000000">&nbsp;</TD>
      <TD align="right" style="border-top: 2px solid #000000">$</TD>
      <TD align="right" style="border-top: 2px solid #000000">290,709.00</TD>
      <TD style="border-top: 2px solid #000000">&nbsp;</TD>
      <TD style="border-right: 2px solid #000000; border-top: 2px solid #000000">&nbsp;</TD>
      <TD style="border-top: 2px solid #000000">&nbsp;</TD>
      <TD align="right" style="border-top: 2px solid #000000">$</TD>
      <TD align="right" style="border-top: 2px solid #000000">34.22</TD>
      <TD style="border-top: 2px solid #000000">&nbsp;</TD>
      <TD width="1%" style="border-top: 2px solid #000000">&nbsp;</TD>
  </TR>
  <TR style="font-size: 1px" valign="bottom">
      <TD nowrap align="left" colspan="23" style="border-top: 3px solid #000000">&nbsp;</TD>
  </TR>
  
  <!-- End Table Body -->
  </TABLE>
  </DIV>
  
  
  
  <TABLE width="100%" border="0" cellpadding="0" cellspacing="0" style="font-size: 10pt">
  <TR>
      <TD width="3%"></TD>
      <TD width="1%"></TD>
      <TD width="96"></TD>
  </TR>
  
  <TR valign="top">
      <TD nowrap align="left">(1)</TD>
      <TD>&nbsp;</TD>
      <TD>This Registration Statement covers an aggregate of 769,920 shares of the Registrant&#146;s common
  stock, par value $.01 per share (the &#147;Common Stock&#148;), that may be issued pursuant to awards
  granted under the equity plans identified above (collectively, the &#147;Plans&#148;). Pursuant to Rule
  416(a) under the Securities Act of 1933, this registration statement also covers such additional
  shares of Common Stock as may be issued in the event of a stock dividend, stock split,
  recapitalization or other similar transaction. In addition, this registration statement covers
  related rights to purchase Series&nbsp;A Junior Participating Preferred Stock, par value $.01 per
  share, registered on a Form 8-A filed with the Securities and Exchange Commission on August&nbsp;7,
  1997 (the &#147;Preferred Stock Purchase Rights&#148;). No separate consideration will be received for the
  Preferred Stock Purchase Rights, which will initially trade together with the Common Stock.</TD>
  </TR>
  
  <TR style="font-size: 3pt"><TD>&nbsp;</TD></TR>
  
  <TR valign="top">
      <TD nowrap align="left">(2)</TD>
      <TD>&nbsp;</TD>
      <TD>Estimated solely for the purpose of determining the registration fee pursuant to Rule 457(h)
  on the basis of the average of the high and low sale prices of the Common Stock on the Nasdaq
  National Market on November&nbsp;9, 2005.</TD>
  </TR>
  
  </TABLE>
  
  
  
  <DIV style="width: 100%; border-bottom: 1pt solid black; margin-top: 10pt; font-size: 1pt">&nbsp;</DIV>
  <DIV style="width: 100%; border-bottom: 2pt solid black; font-size: 1pt">&nbsp;</DIV>
  
  
  
  
  
  
  
  
  
  <P align="center" style="font-size: 10pt">&nbsp;
  </DIV>
  
  <!-- PAGEBREAK -->
  <P><HR noshade><P>
  
  <DIV style="font-family: 'Times New Roman',Times,serif">
  
  
  
  
  
  
  <!-- TOC -->
  <A name="toc"><DIV align="CENTER" style="page-break-before:always"><U><B>TABLE OF CONTENTS</B></U></DIV></A>
  
  <P><CENTER>
  <TABLE border="0" width="90%" cellpadding="0" cellspacing="0">
  <TR>
  	<TD width="3%"></TD>
  	<TD width="3%"></TD>
  	<TD width="3%"></TD>
  	<TD width="3%"></TD>
  	<TD width="3%"></TD>
  	<TD width="3%"></TD>
  	<TD width="3%"></TD>
  	<TD width="3%"></TD>
  	<TD width="76%"></TD>
  </TR>
  <TR><TD></TD><TD colspan="8"><A HREF="#000">Item&nbsp;3. Incorporation of Documents by Reference.</A></TD></TR>
  <TR><TD></TD><TD colspan="8"><A HREF="#001"> Item&nbsp;4. Description of Securities.</A></TD></TR>
  <TR><TD></TD><TD colspan="8"><A HREF="#002"> Item&nbsp;5. Interests of Named Experts and Counsel.</A></TD></TR>
  <TR><TD></TD><TD colspan="8"><A HREF="#003">Item&nbsp;6. Indemnification of Directors and Officers</A></TD></TR>
  <TR><TD></TD><TD colspan="8"><A HREF="#004">Item&nbsp;7. Exemption from Registration Claimed.</A></TD></TR>
  <TR><TD></TD><TD colspan="8"><A HREF="#005">Item&nbsp;8. Exhibits.</A></TD></TR>
  <TR><TD></TD><TD colspan="8"><A HREF="#006">Item&nbsp;9. Undertakings</A></TD></TR>
  <TR><TD colspan="9"><A HREF="#007"> SIGNATURES</A></TD></TR>
  <TR><TD colspan="9"><A HREF="#008"> EXHIBIT INDEX</A></TD></TR>
  <TR><TD colspan="9"><A HREF="b57837s8exv4w1.htm">Helix Technology Corporation 1996 Equity Incentive Plan</A></TD></TR>
  <TR><TD colspan="9"><A HREF="b57837s8exv4w2.htm">Helix Technology Corporation Amended and Restated Stock Option Plan for Non-Employee Directors</A></TD></TR>
  <TR><TD colspan="9"><A HREF="b57837s8exv4w3.htm">Helix Technology Corporation 1981 Employee Stock Option Plan, as Amended</A></TD></TR>
  <TR><TD colspan="9"><A HREF="b57837s8exv5w1.htm">Consent of Thomas S. Grilk, Esq.</A></TD></TR>
  <TR><TD colspan="9"><A HREF="b57837s8exv23w1.htm">Consent of PricewaterhouseCoopers LLP</A></TD></TR>
  </TABLE>
  </CENTER>
  <!-- /TOC -->
  <P><HR noshade><P>
  <H5 align="left" style="page-break-before:always"><A HREF="#toc">Table of Contents</A></H5><P>
  
  
  
  
  
  
  
  <DIV align="center" style="font-size: 10pt; margin-top: 18pt"><B>PART II</B>
  </DIV>
  
  
  <DIV align="center" style="font-size: 10pt; margin-top: 18pt"><B>INFORMATION REQUIRED IN THE REGISTRATION STATEMENT</B>
  </DIV>
  
  <!-- link2 "Item&nbsp;3. Incorporation of Documents by Reference." -->
  <DIV align="left"><A NAME="000"></A></DIV>
  
  <DIV align="left" style="font-size: 10pt; margin-top: 12pt"><B>Item&nbsp;3. Incorporation of Documents by Reference.</B>
  </DIV>
  
  
  <DIV style="margin-top: 6pt">
  <TABLE width="100%" border="0" cellpadding="0" cellspacing="0" style="font-size: 10pt">
  
  <TR valign="top" style="font-size: 10pt; color: #000000; background: transparent">
      <TD width="2%" style="background: transparent">&nbsp;</TD>
      <TD width="3%" nowrap align="left">&nbsp;</TD>
      <TD width="1%">&nbsp;</TD>
      <TD>The Registrant incorporates by reference the following documents filed with the Commission:</TD>
  </TR>
  
  <TR>
      <TD style="font-size: 6pt">&nbsp;</TD>
  </TR><TR valign="top" style="font-size: 10pt; color: #000000; background: transparent">
      <TD width="2%" style="background: transparent">&nbsp;</TD>
      <TD width="3%" nowrap align="left">(a)</TD>
      <TD width="1%">&nbsp;</TD>
      <TD>the Registrant&#146;s Annual Report on Form 10-K for the fiscal year ended September&nbsp;30,
  2004;</TD>
  </TR>
  
  <TR>
      <TD style="font-size: 6pt">&nbsp;</TD>
  </TR><TR valign="top" style="font-size: 10pt; color: #000000; background: transparent">
      <TD width="2%" style="background: transparent">&nbsp;</TD>
      <TD width="3%" nowrap align="left">(b)</TD>
      <TD width="1%">&nbsp;</TD>
      <TD>the Registrant&#146;s Proxy statement on Schedule&nbsp;14A filed with the SEC on January&nbsp;6, 2005;</TD>
  </TR>
  
  <TR>
      <TD style="font-size: 6pt">&nbsp;</TD>
  </TR><TR valign="top" style="font-size: 10pt; color: #000000; background: transparent">
      <TD width="2%" style="background: transparent">&nbsp;</TD>
      <TD width="3%" nowrap align="left">(c)</TD>
      <TD width="1%">&nbsp;</TD>
      <TD>the Registrant&#146;s Quarterly Reports on Form 10-Q for the quarters ended December&nbsp;31,
  2004, March&nbsp;31, 2005 and June&nbsp;30, 2005</TD>
  </TR>
  
  <TR>
      <TD style="font-size: 6pt">&nbsp;</TD>
  </TR><TR valign="top" style="font-size: 10pt; color: #000000; background: transparent">
      <TD width="2%" style="background: transparent">&nbsp;</TD>
      <TD width="3%" nowrap align="left">(d)</TD>
      <TD width="1%">&nbsp;</TD>
      <TD>the Registrant&#146;s Current Reports on Form 8-K filed with the Commission on December&nbsp;28,
  2004, February&nbsp;23, 2005, April&nbsp;29, 2005, July&nbsp;11, 2005, August&nbsp;24, 2005 and October&nbsp;27,
  2005;</TD>
  </TR>
  
  <TR>
      <TD style="font-size: 6pt">&nbsp;</TD>
  </TR><TR valign="top" style="font-size: 10pt; color: #000000; background: transparent">
      <TD width="2%" style="background: transparent">&nbsp;</TD>
      <TD width="3%" nowrap align="left">(e)</TD>
      <TD width="1%">&nbsp;</TD>
      <TD>the description of the Common Stock which is contained in the Registrant&#146;s Registration
  Statement on Form 8-A filed by the Registrant under Section&nbsp;12 of the Securities Exchange
  Act of 1934 on January&nbsp;27, 1995, including any amendments or reports filed for the purpose
  of updating such description; and</TD>
  </TR>
  
  <TR>
      <TD style="font-size: 6pt">&nbsp;</TD>
  </TR><TR valign="top" style="font-size: 10pt; color: #000000; background: transparent">
      <TD width="2%" style="background: transparent">&nbsp;</TD>
      <TD width="3%" nowrap align="left">(f)</TD>
      <TD width="1%">&nbsp;</TD>
      <TD>the description of the Preferred Stock Purchase Rights which is contained in the
  Registrant&#146;s Registration Statement on Form 8-A filed by the Registrant under Section&nbsp;12 of
  the Securities Exchange Act of 1934 on August&nbsp;7, 1997, including any amendments or reports
  filed for the purpose of updating such description.</TD>
  </TR>
  
  </TABLE>
  </DIV>
  
  <DIV align="left" style="font-size: 10pt; margin-top: 6pt">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;In addition, all documents subsequently filed by the Registrant pursuant to Section&nbsp;13(a),
  13(c), 14 or 15(d) of the Securities Exchange Act of 1934, prior to the filing of a post-effective
  amendment which indicates that all securities offered have been sold or which deregisters all
  securities then remaining unsold under this Registration Statement, shall be deemed to be
  incorporated by reference in this Registration Statement and to be a part hereof from the date of
  filing of such documents. Any statement contained herein or in a document incorporated or deemed
  to be incorporated by reference herein shall be deemed to be modified or superceded for purposes of
  this Registration Statement to the extent that a statement contained herein or in any other
  subsequently filed document which also incorporated or is deemed to be incorporated by reference
  herein modifies or supercedes such earlier statement. Any statement so modified or superceded
  shall not be deemed, except as so modified or superceded, to constitute part of this Registration
  Statement.
  </DIV>
  <!-- link2 " Item&nbsp;4. Description of Securities." -->
  <DIV align="left"><A NAME="001"></A></DIV>
  
  <DIV align="left" style="font-size: 10pt; margin-top: 12pt"><B>Item&nbsp;4. Description of Securities.</B>
  </DIV>
  
  
  <DIV align="left" style="font-size: 10pt; margin-top: 6pt">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Not applicable.
  </DIV>
  
  <!-- link2 " Item&nbsp;5. Interests of Named Experts and Counsel." -->
  <DIV align="left"><A NAME="002"></A></DIV>
  
  <DIV align="left" style="font-size: 10pt; margin-top: 12pt"><B>Item&nbsp;5. Interests of Named Experts and Counsel.</B>
  </DIV>
  
  
  <DIV align="left" style="font-size: 10pt; margin-top: 6pt">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The legality of the shares of Common Stock being registered pursuant to this Registration
  Statement will be passed upon for the Registrant by Thomas S. Grilk, Esq., General Counsel of the
  Registrant. Mr.&nbsp;Grilk holds options to purchase Common Stock.
  </DIV>
  
  <!-- link2 "Item&nbsp;6. Indemnification of Directors and Officers" -->
  <DIV align="left"><A NAME="003"></A></DIV>
  
  <DIV align="left" style="font-size: 10pt; margin-top: 12pt"><B>Item&nbsp;6. Indemnification of Directors and Officers</B>
  </DIV>
  
  
  <DIV align="left" style="font-size: 10pt; margin-top: 6pt">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The Registrant is incorporated under the laws of the State of Delaware. Section&nbsp;102 of the
  General Corporation Law of the State of Delaware (the &#147;DGCL&#148;) provides that a Delaware corporation
  may eliminate the personal liability of directors of a corporation to the corporation or its
  stockholders for monetary damages for a breach of fiduciary duty as a director, except where the
  director breached his duty of loyalty, failed to act in good faith, engaged in intentional
  misconduct or knowingly violated a law, authorized the payment of a dividend or approved a stock
  repurchase in violation of Delaware corporate law or obtained an improper personal benefit.
  </DIV>
  
  <DIV align="left" style="font-size: 10pt; margin-top: 6pt">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Section&nbsp;145 of the DGCL provides that a Delaware corporation may indemnify any persons who
  were, are or are threatened to be made parties to any threatened, pending or completed action, suit
  or proceeding, whether civil, criminal, administrative or investigative (other than an action by or
  in the right of such corporation), by reason of the fact that such person is or was an officer,
  director, employee or agent of such corporation, or is or was serving at the request of such
  corporation as a director, officer, employee or agent of another corporation or enterprise. The
  indemnity may include
  </DIV>
  
  <P align="center" style="font-size: 10pt">1
  </DIV>
  
  <!-- PAGEBREAK -->
  <P><HR noshade><P>
  <H5 align="left" style="page-break-before:always"><A HREF="#toc">Table of Contents</A></H5><P>
  
  <DIV style="font-family: 'Times New Roman',Times,serif">
  
  
  
  <DIV align="left" style="font-size: 10pt; margin-top: 6pt">expenses (including attorneys&#146; fees), judgments, fines and amounts paid in settlement actually and
  reasonably incurred by such person in connection with such action, suit or proceeding, provided
  that such person acted in good faith and in a manner he reasonably believed to be in or not opposed
  to the corporation&#146;s best interests and, with respect to any criminal action or proceeding, had no
  reasonable cause to believe that his conduct was illegal.
  </DIV>
  
  <DIV align="left" style="font-size: 10pt; margin-top: 6pt">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Section&nbsp;145 further authorizes a corporation to purchase and maintain insurance on behalf of
  any person who is or was a director, officer, employee or agent of the corporation, or is or was
  serving at the request of the corporation as a director, officer, employee or agent of another
  corporation or enterprise, against any liability asserted against him and incurred by him in any
  such capacity, arising out of his status as such, whether or not the corporation would otherwise
  have the power to indemnify him under Section&nbsp;145.
  </DIV>
  
  <DIV align="left" style="font-size: 10pt; margin-top: 6pt">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The Registrant&#146;s certificate of incorporation provides that its directors shall not be liable
  to the Registrant or its stockholders for monetary damages for breach of fiduciary duty as a
  director, except that directors will be liable to the extent permitted by applicable law for breach
  of the director&#146;s duty of loyalty to the stockholders, actions or omissions not taken in good faith
  or that involve intentional misconduct, pursuant to Section&nbsp;174 of the DGCL or for any transaction
  from which the director derived an improper benefit. The Registrant&#146;s certificate of incorporation
  provides that the Registrant may indemnify its directors and officers to the full extent permitted
  by the laws of the State of Delaware. In addition, the Registrant&#146;s bylaws provide that the
  Registrant may indemnify its officers and directors to the fullest extent permitted by applicable
  law.
  </DIV>
  
  <DIV align="left" style="font-size: 10pt; margin-top: 6pt">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;All of the Registrant&#146;s directors and officers are covered by insurance policies maintained by
  the Registrant against specified liabilities for actions taken in their capacities as such,
  including liabilities under the Securities Act, as amended. In addition, the Registrant has entered
  into indemnification agreements with each of its directors and executive officers that provide for
  indemnification and expense advancement to the fullest extent permitted under the DGCL.
  </DIV>
  <!-- link2 "Item&nbsp;7. Exemption from Registration Claimed." -->
  <DIV align="left"><A NAME="004"></A></DIV>
  
  <DIV align="left" style="font-size: 10pt; margin-top: 12pt"><B>Item&nbsp;7. Exemption from Registration Claimed.</B>
  </DIV>
  
  
  <DIV align="left" style="font-size: 10pt; margin-top: 6pt">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Not applicable.
  </DIV>
  
  <!-- link2 "Item&nbsp;8. Exhibits." -->
  <DIV align="left"><A NAME="005"></A></DIV>
  
  <DIV align="left" style="font-size: 10pt; margin-top: 12pt"><B>Item&nbsp;8. Exhibits.</B>
  </DIV>
  
  
  <DIV align="left" style="font-size: 10pt; margin-top: 6pt">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The following exhibits are filed as part of or incorporated by reference into this Registration Statement:
  </DIV>
  
  <DIV align="center">
  <TABLE style="font-size: 10pt" cellspacing="0" border="0" cellpadding="0" width="90%">
  <!-- Begin Table Head -->
  <TR valign="bottom">
      <TD width="5%">&nbsp;</TD>
      <TD width="2%">&nbsp;</TD>
      <TD width="93%">&nbsp;</TD>
  </TR>
  <!-- End Table Head -->
  <!-- Begin Table Body -->
  <TR valign="bottom">
      <TD valign="top"><DIV style="margin-left:0px; text-indent:-0px">4.1
  </DIV></TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">Helix Technology Corporation 1996 Equity Incentive Plan.</TD>
  </TR>
  <TR valign="bottom">
      <TD valign="top"><DIV style="margin-left:0px; text-indent:-0px">&nbsp;</DIV></TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">&nbsp;</TD>
  </TR>
  <TR valign="bottom">
      <TD valign="top"><DIV style="margin-left:0px; text-indent:-0px">4.2
  </DIV></TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">Helix Technology Corporation Amended and Restated Stock Option Plan for Non-Employee Directors.</TD>
  </TR>
  <TR valign="bottom">
      <TD valign="top"><DIV style="margin-left:0px; text-indent:-0px">&nbsp;</DIV></TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">&nbsp;</TD>
  </TR>
  <TR valign="bottom">
      <TD valign="top"><DIV style="margin-left:0px; text-indent:-0px">4.3
  </DIV></TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">Helix Technology Corporation 1981 Employee Stock Option Plan, as Amended.</TD>
  </TR>
  <TR valign="bottom">
      <TD valign="top"><DIV style="margin-left:0px; text-indent:-0px">&nbsp;</DIV></TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">&nbsp;</TD>
  </TR>
  <TR valign="bottom">
      <TD valign="top"><DIV style="margin-left:0px; text-indent:-0px">5.1
  </DIV></TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">Opinion of Thomas S. Grilk, Esq., General Counsel of the Registrant, as to the legality of the securities being registered.</TD>
  </TR>
  <TR valign="bottom">
      <TD valign="top"><DIV style="margin-left:0px; text-indent:-0px">&nbsp;</DIV></TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">&nbsp;</TD>
  </TR>
  <TR valign="bottom">
      <TD valign="top"><DIV style="margin-left:0px; text-indent:-0px">23.1
  </DIV></TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">Consent of PricewaterhouseCoopers LLP, Independent Registered Public Accounting Firm.</TD>
  </TR>
  <TR valign="bottom">
      <TD valign="top"><DIV style="margin-left:0px; text-indent:-0px">&nbsp;</DIV></TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">&nbsp;</TD>
  </TR>
  <TR valign="bottom">
      <TD valign="top"><DIV style="margin-left:0px; text-indent:-0px">23.2
  </DIV></TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">Consent of Thomas S. Grilk, Esq., General Counsel to the Registrant (contained in the opinion filed as Exhibit&nbsp;5.1 to this Registration Statement).</TD>
  </TR>
  <TR valign="bottom">
      <TD valign="top"><DIV style="margin-left:0px; text-indent:-0px">&nbsp;</DIV></TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">&nbsp;</TD>
  </TR>
  <TR valign="bottom">
  
  <TD valign="top"><DIV style="margin-left:0px; text-indent:-0px">24.1
  </DIV></TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">Power of Attorney (included on signature pages of this Registration Statement).</TD>
  </TR>
  <!-- End Table Body -->
  </TABLE>
  </DIV>
  
  <!-- link2 "Item&nbsp;9. Undertakings" -->
  <DIV align="left"><A NAME="006"></A></DIV>
  
  <DIV align="left" style="font-size: 10pt; margin-top: 12pt"><B>Item&nbsp;9. Undertakings</B>
  </DIV>
  
  <DIV align="left" style="font-size: 10pt; margin-top: 6pt">(a)&nbsp;The Registrant hereby undertakes:
  </DIV>
  
  
  <DIV align="left" style="font-size: 10pt; margin-top: 6pt">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;(1)&nbsp;To file, during any period in which offers or sales are being made, a post-effective
  amendment to this registration statement:
  </DIV>
  
  <DIV align="left" style="font-size: 10pt; margin-top: 6pt">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;(i)&nbsp;To include any prospectus required by Section&nbsp;10(a)(3) of the Securities Act of 1933;
  </DIV>
  
  
  <DIV align="left" style="font-size: 10pt; margin-top: 6pt">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;(ii)&nbsp;To reflect in the prospectus any facts or events arising after the effective date of the
  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 the registration
  statement. Notwithstanding the foregoing, any increase or decrease in volume of
  </div>
  
  <P align="center" style="font-size: 10pt">2
  </DIV>
  
  <!-- PAGEBREAK -->
  <P><HR noshade><P>
  <H5 align="left" style="page-break-before:always"><A HREF="#toc">Table of Contents</A></H5><P>
  
  <DIV style="font-family: 'Times New Roman',Times,serif">
  
  </DIV>
  
  <DIV align="left" style="font-size: 10pt; margin-top: 6pt">securities offered (if the total dollar value of securities offered would not exceed that which was
  registered) and any deviation from the low or high end of the estimated maximum offering range may
  be reflected in the form of prospectus filed with the Commission pursuant to Rule 424(b) if, in the
  aggregate, the changes in volume and price represent no more than a 20&nbsp;percent change in the
  maximum aggregate offering price set forth in the &#147;Calculation of Registration Fee&#148; table in the
  effective registration statement;
  </DIV>
  
  
  <DIV align="left" style="font-size: 10pt; margin-top: 6pt">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;(iii)&nbsp;To include any material information with respect to the plan of distribution not
  previously disclosed in the registration statement or any material change to such information in
  the Registration Statement;
  </DIV>
  
  
  <DIV align="left" style="font-size: 10pt; margin-top: 6pt">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<I>provided, however</I>, that paragraphs (i)&nbsp;and (ii)&nbsp;above do not apply if the information required
  to be included in a post-effective amendment by those paragraphs is contained in periodic reports
  filed with or furnished to the Securities and Exchange Commission by the registrant pursuant to
  Section&nbsp;13 or 15(d) of the Securities Exchange Act of 1934 that are incorporated by reference in
  the registration statement.
  </DIV>
  
  
  <DIV align="left" style="font-size: 10pt; margin-top: 6pt">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;(2)&nbsp;That, for the purpose of determining any liability under the Securities Act of 1933, 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 <I>bona fide </I>offering thereof.
  </DIV>
  
  <DIV align="left" style="font-size: 10pt; margin-top: 6pt">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;(3)&nbsp;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.
  </DIV>
  <DIV align="left" style="font-size: 10pt; margin-top: 6pt">(b)&nbsp;The undersigned registrant hereby undertakes that, for purposes of determining any liability
  under the Securities Act of 1933, each filing of the registrant&#146;s annual report pursuant to Section
  13(a) or 15(d) of the Securities Exchange Act of 1934 (and, where applicable, each filing of an
  employee benefit plan&#146;s annual report pursuant to Section 15(d) of the Securities Exchange Act of
  1934) that is incorporated by reference in the 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 <I>bona fide </I>offering thereof.
  </DIV>
  
  <DIV align="left" style="font-size: 10pt; margin-top: 6pt">(c)&nbsp;Insofar as indemnification for liabilities arising under the Securities Act of 1933 may be
  permitted to directors, officers and controlling persons of the registrant pursuant to the
  foregoing provisions, or otherwise, the registrant has been advised that in the opinion of the
  Securities and Exchange Commission such indemnification is against public policy as expressed in
  the Securities 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 Securities Act of 1933 and will be governed by the final adjudication of such issue.
  </DIV>
  
  
  <P align="center" style="font-size: 10pt">3
  </DIV>
  
  <!-- PAGEBREAK -->
  <P><HR noshade><P>
  <H5 align="left" style="page-break-before:always"><A HREF="#toc">Table of Contents</A></H5><P>
  
  <DIV style="font-family: 'Times New Roman',Times,serif">
  
  
  
  <!-- link1 " SIGNATURES " -->
  <DIV align="left"><A NAME="007"></A></DIV>
  
  <DIV align="center" style="font-size: 10pt; margin-top: 18pt"><B>SIGNATURES</B>
  </DIV>
  
  
  <DIV align="left" style="font-size: 10pt; margin-top: 6pt">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Pursuant to the requirements of the Securities Act of 1933, 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 on Form S-8 to be signed on its behalf by the
  undersigned, thereunto duly authorized in the City of Chelmsford, Massachusetts on November&nbsp;15,
  2005.
  </DIV>
  
  <TABLE width="100%" border="0" cellspacing="0" cellpadding="0" style="font-size: 10pt">
  <TR>
      <TD width="48%">&nbsp;</TD>
      <TD width="1%">&nbsp;</TD>
      <TD width="1%">&nbsp;</TD>
      <TD width="35%">&nbsp;</TD>
      <TD width="15%">&nbsp;</TD>
  </TR>
  <TR>
      <TD valign="top" align="left">&nbsp;</TD>
      <TD colspan="3" align="left"><FONT style="font-variant: SMALL-CAPS"><B>BROOKS AUTOMATION, INC.</B></FONT> <BR>
  &nbsp;</TD>
      <TD>&nbsp;</TD>
  </TR><TR>
      <TD align="left">&nbsp;</TD>
      <TD valign="top">By:&nbsp;&nbsp;</TD>
      <TD colspan="2" style="border-bottom: 1px solid #000000" align="left">/s/ Edward C. Grady
  &nbsp;</TD>
      <TD>&nbsp;</TD>
  </TR>
  <TR>
      <TD align="left">&nbsp;</TD>
      <TD colspan="3" align="left">Edward C. Grady&nbsp;</TD>
      <TD>&nbsp;</TD>
  </TR><TR>
      <TD align="left">&nbsp;</TD>
  
      <TD colspan="3" align="left">Chief Executive Officer and Director&nbsp;</TD>
      <TD>&nbsp;</TD>
  </TR>
  <TR>
      <TD colspan="5">&nbsp;</TD>
  </TR>
  </TABLE>
  
  
  <DIV align="left" style="font-size: 10pt; margin-top: 6pt">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;We, the undersigned officers and directors of Brooks Automation, Inc., hereby severally
  constitute and appoint Thomas S. Grilk, Robert W. Woodbury, Jr. and Edward C. Grady, and each of
  them singly, our true and lawful attorneys-in-fact, with full power to them in any and all
  capacities, to sign any and all amendments to this Registration Statement on Form S-8 (including
  any post-effective amendments), and to file the same, with exhibits thereto and other documents in
  connection therewith, with the Securities and Exchange Commission, hereby ratifying and confirming
  all that each of said attorneys-in-fact may do or cause to be done by virtue hereof.
  </DIV>
  
  <DIV align="left" style="font-size: 10pt; margin-top: 6pt">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Pursuant to the requirements of the Securities Act of 1933, this registration statement has
  been signed by the following persons in the capacities indicated as of November&nbsp;15, 2005.
  </DIV>
  <DIV align="center">
  <TABLE style="font-size: 10pt" cellspacing="0" border="0" cellpadding="0" width="100%">
  <!-- Begin Table Head -->
  <TR valign="bottom">
      <TD width="25%">&nbsp;</TD>
      <TD width="25%">&nbsp;</TD>
      <TD width="30%">&nbsp;</TD>
  </TR>
  
  <TR style="font-size: 8pt" valign="bottom">
      <TD nowrap align="center" style="border-bottom: 1px solid #000000">Signatures</TD>
      <TD>&nbsp;</TD>
      <TD nowrap align="center" style="border-bottom: 1px solid #000000">Title</TD>
  </TR>
  
  <!-- End Table Head -->
  <!-- Begin Table Body -->
  
  <TR valign="bottom" style="padding-top: 1em">
      <TD>&nbsp;</TD>
      <TD>&nbsp;</TD>
      <TD>&nbsp;</TD>
  </tr>
  
  <TR valign="bottom">
      <TD align="center" nowrap valign="top">/s/ Edward C. Grady
  <DIV style="font-size: 1pt; border-bottom: 1px solid #000000">&nbsp;</DIV>
  <FONT style="font-variant: SMALL-CAPS">EDWARD C. GRADY</FONT></TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">
  Chief Executive Officer and Director<br>(Principal Executive Officer)</TD>
  </TR>
  <TR valign="bottom" style="padding-top: 1em">
      <TD align="center" nowrap valign="top">&nbsp;</TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">&nbsp;</TD>
  </TR>
  <TR valign="bottom" style="padding-top: 1em">
      <TD align="center" nowrap valign="top">/s/ Robert W. Woodbury, Jr.
  <DIV style="font-size: 1pt; border-bottom: 1px solid #000000">&nbsp;</DIV>
  ROBERT W. WOODBURY, JR</TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">
  Senior Vice President and Chief Financial Officer<br>(Principal Financial and Accounting Officer)</TD>
  </TR>
  <TR valign="bottom" style="padding-top: 1em">
      <TD align="center" nowrap valign="top">&nbsp;</TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">&nbsp;</TD>
  </TR>
  <TR valign="bottom" style="padding-top: 1em">
      <TD align="center" nowrap valign="top">/s/ A. Clinton Allen
  <DIV style="font-size: 1pt; border-bottom: 1px solid #000000">&nbsp;</DIV>
  A. CLINTON ALLEN</TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">
  Director</TD>
  </TR>
  <TR valign="bottom" style="padding-top: 1em">
      <TD align="center" nowrap valign="top">&nbsp;</TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">&nbsp;</TD>
  </TR>
  <TR valign="bottom" style="padding-top: 1em">
      <TD align="center" nowrap valign="top">/s/ Roger D. Emerick
  <DIV style="font-size: 1pt; border-bottom: 1px solid #000000">&nbsp;</DIV>
  <FONT style="font-variant: SMALL-CAPS">ROGER D. EMERICK</FONT></TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">
  Director</TD>
  </TR>
  <TR valign="bottom" style="padding-top: 1em">
      <TD align="center" nowrap valign="top">&nbsp;</TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">&nbsp;</TD>
  </TR>
  <TR valign="bottom" style="padding-top: 1em">
      <TD align="center" nowrap valign="top">/s/ Amin J. Khoury
  <DIV style="font-size: 1pt; border-bottom: 1px solid #000000">&nbsp;</DIV>
  <FONT style="font-variant: SMALL-CAPS">AMIN J. KHOURY</FONT></TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">
  Director</TD>
  </TR>
  <!-- End Table Body -->
  </TABLE>
  </DIV>
  
  
  <P align="center" style="font-size: 10pt">&nbsp;
  </DIV>
  
  <!-- PAGEBREAK -->
  <P><HR noshade><P>
  <H5 align="left" style="page-break-before:always"><A HREF="#toc">Table of Contents</A></H5><P>
  
  <DIV style="font-family: 'Times New Roman',Times,serif">
  
  <DIV align="center">
  <TABLE style="font-size: 10pt" cellspacing="0" border="0" cellpadding="0" width="100%">
  <!-- Begin Table Head -->
  <TR valign="bottom">
      <TD width="25%">&nbsp;</TD>
      <TD width="25%">&nbsp;</TD>
      <TD width="30%">&nbsp;</TD>
  </TR>
  <TR style="font-size: 8pt" valign="bottom">
      <TD nowrap align="center" style="border-bottom: 1px solid #000000">Signatures</TD>
      <TD>&nbsp;</TD>
      <TD nowrap align="center" style="border-bottom: 1px solid #000000">Title</TD>
  </TR>
  
  <!-- End Table Head -->
  <!-- Begin Table Body -->
  
  <TR valign="bottom" style="padding-top: 1em">
      <TD>&nbsp;</TD>
      <TD>&nbsp;</TD>
      <TD>&nbsp;</TD>
  </tr>
  
  <TR valign="bottom" style="padding-top: 1em">
      <TD align="center" nowrap valign="top">/s/ Joseph R. Martin
  <DIV style="font-size: 1pt; border-bottom: 1px solid #000000">&nbsp;</DIV>
  <FONT style="font-variant: SMALL-CAPS">JOSEPH R. MARTIN</FONT></TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">
  Director</TD>
  </TR>
  <TR valign="bottom" style="padding-top: 1em">
      <TD align="center" nowrap valign="top">&nbsp;</TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">&nbsp;</TD>
  </TR>
  <TR valign="bottom" style="padding-top: 1em">
      <TD align="center" nowrap valign="top">/s/ John K. McGillicuddy
  <DIV style="font-size: 1pt; border-bottom: 1px solid #000000">&nbsp;</DIV>
  <FONT style="font-variant: SMALL-CAPS">JOHN K. MCGILLICUDDY</FONT></TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">
  Director</TD>
  </TR>
  <TR valign="bottom" style="padding-top: 1em">
      <TD align="center" nowrap valign="top">&nbsp;</TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">&nbsp;</TD>
  </TR>
  <TR valign="bottom" style="padding-top: 1em">
      <TD align="center" nowrap valign="top">/s/ Robert J. Therrien
  <DIV style="font-size: 1pt; border-bottom: 1px solid #000000">&nbsp;</DIV>
  <FONT style="font-variant: SMALL-CAPS">ROBERT J. THERRIEN</FONT></TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">
  Director</TD>
  </TR>
  <TR valign="bottom" style="padding-top: 1em">
      <TD align="center" nowrap valign="top">&nbsp;</TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">&nbsp;</TD>
  </TR>
  <TR valign="bottom" style="padding-top: 1em">
      <TD align="center" nowrap valign="top">/s/ Robert J. Lepofsky
  <DIV style="font-size: 1pt; border-bottom: 1px solid #000000">&nbsp;</DIV>
  ROBERT J. LEPOFSKY</TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">
  Director</TD>
  </TR>
  <TR valign="bottom" style="padding-top: 1em">
      <TD align="center" nowrap valign="top">&nbsp;</TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">&nbsp;</TD>
  </TR>
  <TR valign="bottom" style="padding-top: 1em">
      <TD align="center" nowrap valign="top">/s/ Alfred Woollacott, III
  <DIV style="font-size: 1pt; border-bottom: 1px solid #000000">&nbsp;</DIV>
  ALFRED WOOLLACOTT, III</TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">
  Director</TD>
  </TR>
  <TR valign="bottom" style="padding-top: 1em">
      <TD align="center" nowrap valign="top">&nbsp;</TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">&nbsp;</TD>
  </TR>
  <TR valign="bottom" style="padding-top: 1em">
      <TD align="center" nowrap valign="top">/s/ Mark S. Wrighton
  <DIV style="font-size: 1pt; border-bottom: 1px solid #000000">&nbsp;</DIV>
  MARK S. WRIGHTON</TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">
  Director</TD>
  </TR>
  <!-- End Table Body -->
  </TABLE>
  </DIV>
  
  
  <P align="center" style="font-size: 10pt">&nbsp;
  </DIV>
  
  <!-- PAGEBREAK -->
  <P><HR noshade><P>
  <H5 align="left" style="page-break-before:always"><A HREF="#toc">Table of Contents</A></H5><P>
  
  <DIV style="font-family: 'Times New Roman',Times,serif">
  
  <!-- link1 " EXHIBIT INDEX" -->
  <DIV align="left"><A NAME="008"></A></DIV>
  
  <DIV align="center" style="font-size: 10pt; margin-top: 18pt"><U>EXHIBIT INDEX</U>
  </DIV>
  
  <DIV align="center">
  <TABLE style="font-size: 10pt" cellspacing="0" border="0" cellpadding="0" width="100%">
  <!-- Begin Table Head -->
  <TR valign="bottom">
      <TD width="5%">&nbsp;</TD>
      <TD width="2%">&nbsp;</TD>
      <TD width="93%">&nbsp;</TD>
  </TR>
  <!-- End Table Head -->
  <!-- Begin Table Body -->
  <TR valign="bottom">
      <TD valign="top"><DIV style="margin-left:0px; text-indent:-0px">4.1
  </DIV></TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">Helix Technology Corporation 1996 Equity Incentive Plan.</TD>
  </TR>
  <TR valign="bottom">
      <TD valign="top"><DIV style="margin-left:0px; text-indent:-0px">&nbsp;</DIV></TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">&nbsp;</TD>
  </TR>
  <TR valign="bottom">
      <TD valign="top"><DIV style="margin-left:0px; text-indent:-0px">4.2
  </DIV></TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">Helix Technology Corporation Amended and Restated Stock Option Plan for Non-Employee Directors.</TD>
  </TR>
  <TR valign="bottom">
      <TD valign="top"><DIV style="margin-left:0px; text-indent:-0px">&nbsp;</DIV></TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">&nbsp;</TD>
  </TR>
  <TR valign="bottom">
      <TD valign="top"><DIV style="margin-left:0px; text-indent:-0px">4.3
  </DIV></TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">Helix Technology Corporation 1981 Employee Stock Option Plan, as Amended</TD>
  </TR>
  <TR valign="bottom">
      <TD valign="top"><DIV style="margin-left:0px; text-indent:-0px">&nbsp;</DIV></TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">&nbsp;</TD>
  </TR>
  <TR valign="bottom">
      <TD valign="top"><DIV style="margin-left:0px; text-indent:-0px">5.1
  </DIV></TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">Opinion of Thomas S. Grilk, Esq., General Counsel of the Registrant, as to the legality of the securities being registered.</TD>
  </TR>
  <TR valign="bottom">
      <TD valign="top"><DIV style="margin-left:0px; text-indent:-0px">&nbsp;</DIV></TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">&nbsp;</TD>
  </TR>
  <TR valign="bottom">
      <TD valign="top"><DIV style="margin-left:0px; text-indent:-0px">23.1
  </DIV></TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">Consent of PricewaterhouseCoopers LLP, Independent Registered Public Accounting Firm.</TD>
  </TR>
  <TR valign="bottom">
      <TD valign="top"><DIV style="margin-left:0px; text-indent:-0px">&nbsp;</DIV></TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">&nbsp;</TD>
  </TR>
  <TR valign="bottom">
      <TD valign="top"><DIV style="margin-left:0px; text-indent:-0px">23.2
  </DIV></TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">Consent of Thomas S. Grilk, Esq., General Counsel to the Registrant (contained in the opinion filed as Exhibit&nbsp;5.1 to this Registration Statement).</TD>
  </TR>
  <TR valign="bottom">
      <TD valign="top"><DIV style="margin-left:0px; text-indent:-0px">&nbsp;</DIV></TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">&nbsp;</TD>
  </TR>
  <TR valign="bottom">
      <TD valign="top"><DIV style="margin-left:0px; text-indent:-0px">24.1
  </DIV></TD>
      <TD>&nbsp;</TD>
      <TD align="left" valign="top">Power of Attorney (included on signature pages of this Registration Statement).</TD>
  </TR>
  <!-- End Table Body -->
  </TABLE>
  </DIV>
  
  
  
  <P align="center" style="font-size: 10pt">&nbsp;
  </DIV>
  
  </BODY>
  </HTML>
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text: sv8
  Table of Contents
  As filed with the Securities and Exchange Commission on November 15, 2005
  Registration No. 333-____________
  SECURITIES AND EXCHANGE COMMISSION
  WASHINGTON, D.C. 20549
  FORM S-8
  REGISTRATION STATEMENT
  UNDER
  THE SECURITIES ACT OF 1933
  BROOKS AUTOMATION, INC.
  (Exact Name of Registrant as Specified in its Charter)
  Delaware
  (State or Other Jurisdiction of Incorporation or Organization)
  04-3040660
  (I.R.S. Employer Identification Number)
  15 Elizabeth Drive, Chelmsford, MA 01824
  (Address of Principal Executive Offices)
  Helix Technology Corporation 1996 Equity Incentive Plan
  Helix Technology Corporation Amended and Restated Stock Option Plan for Non-Employee Directors
  Helix Technology Corporation 1981 Employee Stock Option Plan, as Amended
  (Full Title of the Plans)
  Thomas S. Grilk
  Senior Vice President, General Counsel and Secretary
  Brooks Automation, Inc.
  15 Elizabeth Drive
  Chelmsford, MA 01824
  (Name and Address of Agent for Service)
  (978) 721-3371
  (Telephone Number, Including Area Code for Agent for Service)
  CALCULATION OF REGISTRATION FEE
  Proposed Maximum
  Proposed
  Amount of
  Title of Securities to be
  Amount to be
  Offering Price Per
  Maximum Aggregate
  Registration
  Registered
  Registered (1)
  Share (2)
  Offering Price (2)
  Fee (2)
  Helix Technology
  Corporation 1996 Equity
  Incentive Plan
  721,080
  $
  13.095
  $
  9,442,542.60
  $
  1,111.39
  Helix Technology
  Corporation Amended and
  Restated Stock Option
  Plan for Non-Employee
  Directors
  26,640
  $
  13.095
  $
  348,850.80
  $
  41.06
  Helix Technology
  Corporation 1981
  Employee Stock Option
  Plan, as Amended
  22,200
  $
  13.095
  $
  290,709.00
  $
  34.22
  (1)
  This Registration Statement covers an aggregate of 769,920 shares of the Registrant's common
  stock, par value $.01 per share (the "Common Stock"), that may be issued pursuant to awards
  granted under the equity plans identified above (collectively, the "Plans"). Pursuant to Rule
  416(a) under the Securities Act of 1933, this registration statement also covers such additional
  shares of Common Stock as may be issued in the event of a stock dividend, stock split,
  recapitalization or other similar transaction. In addition, this registration statement covers
  related rights to purchase Series A Junior Participating Preferred Stock, par value $.01 per
  share, registered on a Form 8-A filed with the Securities and Exchange Commission on August 7,
  1997 (the "Preferred Stock Purchase Rights"). No separate consideration will be received for the
  Preferred Stock Purchase Rights, which will initially trade together with the Common Stock.
  (2)
  Estimated solely for the purpose of determining the registration fee pursuant to Rule 457(h)
  on the basis of the average of the high and low sale prices of the Common Stock on the Nasdaq
  National Market on November 9, 2005.
  TABLE OF CONTENTS
  Item 3. Incorporation of Documents by Reference.
  Item 4. Description of Securities.
  Item 5. Interests of Named Experts and Counsel.
  Item 6. Indemnification of Directors and Officers
  Item 7. Exemption from Registration Claimed.
  Item 8. Exhibits.
  Item 9. Undertakings
  SIGNATURES
  EXHIBIT INDEX
  Helix Technology Corporation 1996 Equity Incentive Plan
  Helix Technology Corporation Amended and Restated Stock Option Plan for Non-Employee Directors
  Helix Technology Corporation 1981 Employee Stock Option Plan, as Amended
  Consent of Thomas S. Grilk, Esq.
  Consent of PricewaterhouseCoopers LLP
  Table of Contents
  PART II
  INFORMATION REQUIRED IN THE REGISTRATION STATEMENT
  Item 3. Incorporation of Documents by Reference.
  The Registrant incorporates by reference the following documents filed with the Commission:
  (a)
  the Registrant's Annual Report on Form 10-K for the fiscal year ended September 30,
  2004;
  (b)
  the Registrant's Proxy statement on Schedule 14A filed with the SEC on January 6, 2005;
  (c)
  the Registrant's Quarterly Reports on Form 10-Q for the quarters ended December 31,
  2004, March 31, 2005 and June 30, 2005
  (d)
  the Registrant's Current Reports on Form 8-K filed with the Commission on December 28,
  2004, February 23, 2005, April 29, 2005, July 11, 2005, August 24, 2005 and October 27,
  2005;
  (e)
  the description of the Common Stock which is contained in the Registrant's Registration
  Statement on Form 8-A filed by the Registrant under Section 12 of the Securities Exchange
  Act of 1934 on January 27, 1995, including any amendments or reports filed for the purpose
  of updating such description; and
  (f)
  the description of the Preferred Stock Purchase Rights which is contained in the
  Registrant's Registration Statement on Form 8-A filed by the Registrant under Section 12 of
  the Securities Exchange Act of 1934 on August 7, 1997, including any amendments or reports
  filed for the purpose of updating such description.
  In addition, all documents subsequently filed by the Registrant pursuant to Section 13(a),
  13(c), 14 or 15(d) of the Securities Exchange Act of 1934, prior to the filing of a post-effective
  amendment which indicates that all securities offered have been sold or which deregisters all
  securities then remaining unsold under this Registration Statement, shall be deemed to be
  incorporated by reference in this Registration Statement and to be a part hereof from the date of
  filing of such documents. Any statement contained herein or in a document incorporated or deemed
  to be incorporated by reference herein shall be deemed to be modified or superceded for purposes of
  this Registration Statement to the extent that a statement contained herein or in any other
  subsequently filed document which also incorporated or is deemed to be incorporated by reference
  herein modifies or supercedes such earlier statement. Any statement so modified or superceded
  shall not be deemed, except as so modified or superceded, to constitute part of this Registration
  Statement.
  Item 4. Description of Securities.
  Not applicable.
  Item 5. Interests of Named Experts and Counsel.
  The legality of the shares of Common Stock being registered pursuant to this Registration
  Statement will be passed upon for the Registrant by Thomas S. Grilk, Esq., General Counsel of the
  Registrant. Mr. Grilk holds options to purchase Common Stock.
  Item 6. Indemnification of Directors and Officers
  The Registrant is incorporated under the laws of the State of Delaware. Section 102 of the
  General Corporation Law of the State of Delaware (the "DGCL") provides that a Delaware corporation
  may eliminate the personal liability of directors of a corporation to the corporation or its
  stockholders for monetary damages for a breach of fiduciary duty as a director, except where the
  director breached his duty of loyalty, failed to act in good faith, engaged in intentional
  misconduct or knowingly violated a law, authorized the payment of a dividend or approved a stock
  repurchase in violation of Delaware corporate law or obtained an improper personal benefit.
  Section 145 of the DGCL provides that a Delaware corporation may indemnify any persons who
  were, are or are threatened to be made parties to any threatened, pending or completed action, suit
  or proceeding, whether civil, criminal, administrative or investigative (other than an action by or
  in the right of such corporation), by reason of the fact that such person is or was an officer,
  director, employee or agent of such corporation, or is or was serving at the request of such
  corporation as a director, officer, employee or agent of another corporation or enterprise. The
  indemnity may include
  1
  Table of Contents
  expenses (including attorneys' fees), judgments, fines and amounts paid in settlement actually and
  reasonably incurred by such person in connection with such action, suit or proceeding, provided
  that such person acted in good faith and in a manner he reasonably believed to be in or not opposed
  to the corporation's best interests and, with respect to any criminal action or proceeding, had no
  reasonable cause to believe that his conduct was illegal.
  Section 145 further authorizes a corporation to purchase and maintain insurance on behalf of
  any person who is or was a director, officer, employee or agent of the corporation, or is or was
  serving at the request of the corporation as a director, officer, employee or agent of another
  corporation or enterprise, against any liability asserted against him and incurred by him in any
  such capacity, arising out of his status as such, whether or not the corporation would otherwise
  have the power to indemnify him under Section 145.
  The Registrant's certificate of incorporation provides that its directors shall not be liable
  to the Registrant or its stockholders for monetary damages for breach of fiduciary duty as a
  director, except that directors will be liable to the extent permitted by applicable law for breach
  of the director's duty of loyalty to the stockholders, actions or omissions not taken in good faith
  or that involve intentional misconduct, pursuant to Section 174 of the DGCL or for any transaction
  from which the director derived an improper benefit. The Registrant's certificate of incorporation
  provides that the Registrant may indemnify its directors and officers to the full extent permitted
  by the laws of the State of Delaware. In addition, the Registrant's bylaws provide that the
  Registrant may indemnify its officers and directors to the fullest extent permitted by applicable
  law.
  All of the Registrant's directors and officers are covered by insurance policies maintained by
  the Registrant against specified liabilities for actions taken in their capacities as such,
  including liabilities under the Securities Act, as amended. In addition, the Registrant has entered
  into indemnification agreements with each of its directors and executive officers that provide for
  indemnification and expense advancement to the fullest extent permitted under the DGCL.
  Item 7. Exemption from Registration Claimed.
  Not applicable.
  Item 8. Exhibits.
  The following exhibits are filed as part of or incorporated by reference into this Registration Statement:
  4.1
  Helix Technology Corporation 1996 Equity Incentive Plan.
  4.2
  Helix Technology Corporation Amended and Restated Stock Option Plan for Non-Employee Directors.
  4.3
  Helix Technology Corporation 1981 Employee Stock Option Plan, as Amended.
  5.1
  Opinion of Thomas S. Grilk, Esq., General Counsel of the Registrant, as to the legality of the securities being registered.
  23.1
  Consent of PricewaterhouseCoopers LLP, Independent Registered Public Accounting Firm.
  23.2
  Consent of Thomas S. Grilk, Esq., General Counsel to the Registrant (contained in the opinion filed as Exhibit 5.1 to this Registration Statement).
  24.1
  Power of Attorney (included on signature pages of this Registration Statement).
  Item 9. Undertakings
  (a) The 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;
  (ii) To reflect in the prospectus any facts or events arising after the effective date of the
  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 the registration
  statement. Notwithstanding the foregoing, any increase or decrease in volume of
  2
  Table of Contents
  securities offered (if the total dollar value of securities offered would not exceed that which was
  registered) and any deviation from the low or high end of the estimated maximum offering range may
  be reflected in the form of prospectus filed with the Commission pursuant to Rule 424(b) if, in the
  aggregate, the changes in volume and price represent no more than a 20 percent change in the
  maximum aggregate offering price set forth in the "Calculation of Registration Fee" table in the
  effective registration statement;
  (iii) To include any material information with respect to the plan of distribution not
  previously disclosed in the registration statement or any material change to such information in
  the Registration Statement;
  provided, however
  , that paragraphs (i) and (ii) above do not apply if the information required
  to be included in a post-effective amendment by those paragraphs is contained in periodic reports
  filed with or furnished to the Securities and Exchange Commission by the registrant pursuant to
  Section 13 or 15(d) of the Securities Exchange Act of 1934 that are incorporated by reference in
  the registration statement.
  (2) That, for the purpose of determining any liability under the Securities Act of 1933, 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.
  (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 Securities Act of 1933, each filing of the registrant's annual report pursuant to Section
  13(a) or 15(d) of the Securities Exchange Act of 1934 (and, where applicable, each filing of an
  employee benefit plan's annual report pursuant to Section 15(d) of the Securities Exchange Act of
  1934) that is incorporated by reference in the 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 Securities Act of 1933 may be
  permitted to directors, officers and controlling persons of the registrant pursuant to the
  foregoing provisions, or otherwise, the registrant has been advised that in the opinion of the
  Securities and Exchange Commission such indemnification is against public policy as expressed in
  the Securities 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 Securities Act of 1933 and will be governed by the final adjudication of such issue.
  3
  Table of Contents
  SIGNATURES
  Pursuant to the requirements of the Securities Act of 1933, 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 on Form S-8 to be signed on its behalf by the
  undersigned, thereunto duly authorized in the City of Chelmsford, Massachusetts on November 15,
  2005.
  BROOKS AUTOMATION, INC.
  By:
  /s/ Edward C. Grady
  Edward C. Grady
  Chief Executive Officer and Director
  We, the undersigned officers and directors of Brooks Automation, Inc., hereby severally
  constitute and appoint Thomas S. Grilk, Robert W. Woodbury, Jr. and Edward C. Grady, and each of
  them singly, our true and lawful attorneys-in-fact, with full power to them in any and all
  capacities, to sign any and all amendments to this Registration Statement on Form S-8 (including
  any post-effective amendments), and to file the same, with exhibits thereto and other documents in
  connection therewith, with the Securities and Exchange Commission, hereby ratifying and confirming
  all that each of said attorneys-in-fact may do or cause to be done by virtue hereof.
  Pursuant to the requirements of the Securities Act of 1933, this registration statement has
  been signed by the following persons in the capacities indicated as of November 15, 2005.
  Signatures
  Title
  /s/ Edward C. Grady
  EDWARD C. GRADY
  Chief Executive Officer and Director
  (Principal Executive Officer)
  /s/ Robert W. Woodbury, Jr.
  ROBERT W. WOODBURY, JR
  Senior Vice President and Chief Financial Officer
  (Principal Financial and Accounting Officer)
  /s/ A. Clinton Allen
  A. CLINTON ALLEN
  Director
  /s/ Roger D. Emerick
  ROGER D. EMERICK
  Director
  /s/ Amin J. Khoury
  AMIN J. KHOURY
  Director
  Table of Contents
  Signatures
  Title
  /s/ Joseph R. Martin
  JOSEPH R. MARTIN
  Director
  /s/ John K. McGillicuddy
  JOHN K. MCGILLICUDDY
  Director
  /s/ Robert J. Therrien
  ROBERT J. THERRIEN
  Director
  /s/ Robert J. Lepofsky
  ROBERT J. LEPOFSKY
  Director
  /s/ Alfred Woollacott, III
  ALFRED WOOLLACOTT, III
  Director
  /s/ Mark S. Wrighton
  MARK S. WRIGHTON
  Director
  Table of Contents
  EXHIBIT INDEX
  4.1
  Helix Technology Corporation 1996 Equity Incentive Plan.
  4.2
  Helix Technology Corporation Amended and Restated Stock Option Plan for Non-Employee Directors.
  4.3
  Helix Technology Corporation 1981 Employee Stock Option Plan, as Amended
  5.1
  Opinion of Thomas S. Grilk, Esq., General Counsel of the Registrant, as to the legality of the securities being registered.
  23.1
  Consent of PricewaterhouseCoopers LLP, Independent Registered Public Accounting Firm.
  23.2
  Consent of Thomas S. Grilk, Esq., General Counsel to the Registrant (contained in the opinion filed as Exhibit 5.1 to this Registration Statement).
  24.1
  Power of Attorney (included on signature pages of this Registration Statement).