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<DIV style="font-family: 'Times New Roman',Times,serif">


<DIV align="center" style="font-size: 10pt; margin-top: 18pt"><B>As
filed with the Securities and Exchange Commission on May&nbsp;10, 2007</B>
</DIV>


<DIV align="right" style="font-size: 10pt; margin-top: 12pt"><B>Registration No.&nbsp;333</B>
</DIV>


<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: 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" style="font-size: 10pt; margin-top: 18pt"><DIV align="center"><DIV style="font-size: 3pt; margin-top: 16pt; width: 26%; border-top: 1px solid #000000">&nbsp;</DIV></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>TOMOTHERAPY INCORPORATED</B>
</DIV>

<DIV align="center" style="font-size: 10pt">(Exact name of registrant as specified in its charter)</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="47%">&nbsp;</TD>
    <TD width="5%">&nbsp;</TD>
    <TD width="47%">&nbsp;</TD>
</TR>
<!-- End Table Head -->
<!-- Begin Table Body -->
<TR valign="bottom">
    <TD align="center" valign="top"><B>Wisconsin</B><BR>
(State or Other Jurisdiction of <BR>
Incorporation or Organization)
</TD>
    <TD>&nbsp;</TD>
    <TD align="center" valign="top"><B>39-1914727</B><BR>
(I.R.S. Employer<BR>
Identification Number)</TD>
</TR>
<!-- End Table Body -->
</TABLE>
</DIV>


<DIV align="center" style="font-size: 10pt; margin-top: 18pt"><DIV align="center"><DIV style="font-size: 3pt; margin-top: 16pt; width: 26%; border-top: 1px solid #000000">&nbsp;</DIV></DIV>
</DIV>


<DIV align="center" style="font-size: 10pt; margin-top: 18pt"><B>1240 Deming Way<BR>
Madison, Wisconsin 53717</B><BR>
(Address of Principal Executive Offices including Zip Code)
</DIV>


<DIV align="center" style="font-size: 10pt; margin-top: 18pt"><DIV align="center"><DIV style="font-size: 3pt; margin-top: 16pt; width: 26%; border-top: 1px solid #000000">&nbsp;</DIV></DIV>
</DIV>


<DIV align="center" style="font-size: 12pt; margin-top: 18pt"><B>TomoTherapy Incorporated Incentive Stock Option Plan<BR>
TomoTherapy Incorporated 2000 Stock Option Plan<BR>
Tomotherapy Incorporated 2002 Stock Option Plan</B>
</DIV>


<DIV align="Center" style="font-size: 10pt; margin-top: 6pt">(Full Title of the Plan)

</DIV>

<DIV align="center" style="font-size: 10pt; margin-top: 18pt"><DIV align="center"><DIV style="font-size: 3pt; margin-top: 16pt; width: 26%; border-top: 1px solid #000000">&nbsp;</DIV></DIV>
</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="47%">&nbsp;</TD>
    <TD width="5%">&nbsp;</TD>
    <TD width="47%">&nbsp;</TD>
</TR>
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<!-- Begin Table Body -->
<TR valign="bottom">
    <TD align="center" valign="top"><B>Stephen C. Hathaway</B>
</TD>
    <TD>&nbsp;</TD>
    <TD align="center" valign="top"><B>Copy to:</B></TD>
</TR>
<TR valign="bottom">
    <TD align="center" valign="top"><B>Chief Financial Officer and Treasurer</B><BR>
TomoTherapy Incorporated <BR>
1240 Deming Way <BR>
Madison, Wisconsin 53717<BR>
(608)&nbsp;824-2800
</TD>
    <TD>&nbsp;</TD>
    <TD align="center" valign="top"><B>Geoffrey R. Morgan, Esq.</B><BR>
Michael Best &#038; Friedrich, LLP<BR>
100 East Wisconsin Avenue<BR>
Milwaukee, Wisconsin 53202<BR>
(414)&nbsp;225-2752</TD>
</TR>
<!-- End Table Body -->
</TABLE>
</DIV>

<DIV align="center" style="font-size: 10pt">(Name and Address, Including Zip Code, and Telephone Number,<BR>
Including Area Code, of 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="36%">&nbsp;</TD>
    <TD width="8%">&nbsp;</TD>
    <TD width="5%">&nbsp;</TD>
    <TD width="1%">&nbsp;</TD>
    <TD width="5%">&nbsp;</TD>
    <TD width="4%">&nbsp;</TD>
    <TD width="11%">&nbsp;</TD>
    <TD width="4%">&nbsp;</TD>
    <TD width="11%">&nbsp;</TD>
    <TD width="4%">&nbsp;</TD>
    <TD width="11%">&nbsp;</TD>
</TR>
<TR style="font-size: 1px">
    <TD colspan="11" valign="top" align="left" style="border-top: 3px double #000000">&nbsp;</TD>
</TR>

<TR style="font-size: 8pt" valign="bottom">
    <TD>&nbsp;</TD>
    <TD>&nbsp;</TD>
    <TD>&nbsp;</TD>
    <TD>&nbsp;</TD>
    <TD>&nbsp;</TD>
    <TD>&nbsp;</TD>
    <TD nowrap align="center"><B>Proposed</B></TD>
    <TD>&nbsp;</TD>
    <TD nowrap align="center"><B>Proposed</B></TD>
    <TD>&nbsp;</TD>
    <TD nowrap align="center">&nbsp;</TD>
</TR>
<TR style="font-size: 8pt" valign="bottom">
    <TD>&nbsp;</TD>
    <TD>&nbsp;</TD>
    <TD>&nbsp;</TD>
    <TD>&nbsp;</TD>
    <TD>&nbsp;</TD>
    <TD>&nbsp;</TD>
    <TD nowrap align="center"><B>Maximum</B></TD>
    <TD>&nbsp;</TD>
    <TD nowrap align="center"><B>Maximum</B></TD>
    <TD>&nbsp;</TD>
    <TD nowrap align="center">&nbsp;</TD>
</TR>
<TR style="font-size: 8pt" valign="bottom">
    <TD nowrap align="center"><B>Title Of</B></TD>
    <TD>&nbsp;</TD>
    <TD nowrap align="center" colspan="3"><B>Amount</B></TD>
    <TD>&nbsp;</TD>
    <TD nowrap align="center"><B>Offering</B></TD>
    <TD>&nbsp;</TD>
    <TD nowrap align="center"><B>Aggregate</B></TD>
    <TD>&nbsp;</TD>
    <TD nowrap align="center"><B>Amount Of</B></TD>
</TR>
<TR style="font-size: 8pt" valign="bottom">
    <TD nowrap align="center"><B>Securities To Be</B></TD>
    <TD>&nbsp;</TD>
    <TD nowrap align="center" colspan="3"><B>To Be</B></TD>
    <TD>&nbsp;</TD>
    <TD nowrap align="center"><B>Price Per</B></TD>
    <TD>&nbsp;</TD>
    <TD nowrap align="center"><B>Offering</B></TD>
    <TD>&nbsp;</TD>
    <TD nowrap align="center"><B>Registration</B></TD>
</TR>
<TR style="font-size: 8pt" valign="bottom">
    <TD nowrap align="center"><B>Registered</B></TD>
    <TD>&nbsp;</TD>
    <TD nowrap align="center" colspan="3"><B>Registered(1)</B></TD>
    <TD>&nbsp;</TD>
    <TD nowrap align="center"><B>Share</B></TD>
    <TD>&nbsp;</TD>
    <TD nowrap align="center"><B>Price</B></TD>
    <TD>&nbsp;</TD>
    <TD nowrap align="center"><B>Fee</B></TD>
</TR>

<!-- End Table Head -->
<!-- Begin Table Body -->
<TR style="font-size: 1px">
    <TD colspan="11" valign="top" align="left" style="border-top: 1px solid #000000">&nbsp;</TD>
</TR>
<TR valign="bottom"><!-- Blank Space -->
    <TD valign="top"><DIV style="margin-left:0px; text-indent:-0px">&nbsp;</DIV></TD>
    <TD>&nbsp;</TD>
    <TD nowrap align="right" valign="top">&nbsp;</TD>
    <TD align="right" valign="top">&nbsp;</TD>
    <TD valign="top">&nbsp;</TD>
    <TD>&nbsp;</TD>
    <TD align="center" valign="top">&nbsp;</TD>
    <TD>&nbsp;</TD>
    <TD align="center" valign="top">&nbsp;</TD>
    <TD>&nbsp;</TD>
    <TD align="center" valign="top">&nbsp;</TD>
</TR>
<TR valign="bottom">
    <TD valign="top"><DIV style="margin-left:0px; text-indent:-0px">Common Stock,
par value $0.01 per
share
</DIV></TD>
    <TD>&nbsp;</TD>
    <TD nowrap align="right" valign="top">&nbsp;</TD>
    <TD align="right" valign="top">73,304</TD>
    <TD nowrap valign="top">(2)</TD>
    <TD>&nbsp;</TD>
    <TD align="center" valign="top">$0.11(3)
</TD>
    <TD>&nbsp;</TD>
    <TD align="center" valign="top">$22,725
</TD>
    <TD>&nbsp;</TD>
    <TD align="center" valign="top">$.25</TD>
</TR>
<TR valign="bottom"><!-- Blank Space -->
    <TD valign="top"><DIV style="margin-left:0px; text-indent:-0px">&nbsp;</DIV></TD>
    <TD>&nbsp;</TD>
    <TD nowrap align="right" valign="top">&nbsp;</TD>
    <TD align="right" valign="top">&nbsp;</TD>
    <TD valign="top">&nbsp;</TD>
    <TD>&nbsp;</TD>
    <TD align="center" valign="top">&nbsp;</TD>
    <TD>&nbsp;</TD>
    <TD align="center" valign="top">&nbsp;</TD>
    <TD>&nbsp;</TD>
    <TD align="center" valign="top">&nbsp;</TD>
</TR>
<TR valign="bottom">
    <TD valign="top"><DIV style="margin-left:0px; text-indent:-0px">Common Stock,
par value $0.01 per
share
</DIV></TD>
    <TD>&nbsp;</TD>
    <TD nowrap align="right" valign="top">&nbsp;</TD>
    <TD align="right" valign="top">113,424</TD>
    <TD nowrap valign="top">(4)</TD>
    <TD>&nbsp;</TD>
    <TD align="center" valign="top">$0.31(5)
</TD>
    <TD>&nbsp;</TD>
    <TD align="center" valign="top">$35,162
</TD>
    <TD>&nbsp;</TD>
    <TD align="center" valign="top">$1.08</TD>
</TR>
<TR valign="bottom"><!-- Blank Space -->
    <TD valign="top"><DIV style="margin-left:0px; text-indent:-0px">&nbsp;</DIV></TD>
    <TD>&nbsp;</TD>
    <TD nowrap align="right" valign="top">&nbsp;</TD>
    <TD align="right" valign="top">&nbsp;</TD>
    <TD valign="top">&nbsp;</TD>
    <TD>&nbsp;</TD>
    <TD align="center" valign="top">&nbsp;</TD>
    <TD>&nbsp;</TD>
    <TD align="center" valign="top">&nbsp;</TD>
    <TD>&nbsp;</TD>
    <TD align="center" valign="top">&nbsp;</TD>
</TR>
<TR valign="bottom">
    <TD valign="top"><DIV style="margin-left:0px; text-indent:-0px">Common Stock, par
value $0.01 per
share
</DIV></TD>
    <TD>&nbsp;</TD>
    <TD nowrap align="right" valign="top">&nbsp;</TD>
    <TD align="right" valign="top">6,811,115</TD>
    <TD nowrap valign="top">(6)</TD>
    <TD>&nbsp;</TD>
    <TD align="center" valign="top">$4.19(7)
</TD>
    <TD>&nbsp;</TD>
    <TD align="center" valign="top">$28,538,572
</TD>
    <TD>&nbsp;</TD>
    <TD align="center" valign="top">$877.50</TD>
</TR>
<TR style="font-size: 1px">
    <TD colspan="11" valign="top" align="left" style="border-top: 3px double #000000">&nbsp;</TD>
</TR>
<!-- End Table Body -->
</TABLE>
</DIV>



<DIV align="left">
<DIV style="font-size: 3pt; margin-top: 12pt; width: 18%; border-top: 0px solid #000000">&nbsp;</DIV>
</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 shall also cover any additional shares of Common Stock
which become issuable under any of the plans being registered pursuant to this Registration
Statement by reason of any stock dividend, stock split, recapitalization or any other similar
transaction effected without the receipt of consideration which results in an increase in the
number of the Registrant&#146;s outstanding shares of 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>Represents 73,304 shares of Common Stock reserved for issuance upon exercise of outstanding
options granted under the TomoTherapy Incentive Stock Option Plan.</TD>
</TR>

<TR style="font-size: 3pt"><TD>&nbsp;</TD></TR>

<TR valign="top">
    <TD nowrap align="left">(3)</TD>
    <TD>&nbsp;</TD>
    <TD>Estimated solely for the purpose of calculating the registration fee pursuant to Rule 457(h)
under the Securities Act of 1933, as amended, on the basis of the weighted average exercise
price of the options granted under the TomoTherapy Incorporated Incentive Stock Option Plan.</TD>
</TR>

<TR style="font-size: 3pt"><TD>&nbsp;</TD></TR>

<TR valign="top">
    <TD nowrap align="left">(4)</TD>
    <TD>&nbsp;</TD>
    <TD>Represents 113,424 shares of Common Stock reserved for issuance upon exercise of outstanding
options granted under the TomoTherapy Incorporated 2000 Stock Option Plan.</TD>
</TR>

<TR style="font-size: 3pt"><TD>&nbsp;</TD></TR>

<TR valign="top">
    <TD nowrap align="left">(5)</TD>
    <TD>&nbsp;</TD>
    <TD>Estimated solely for the purpose of calculating the registration fee pursuant to Rule 457(h)
under the Securities Act of 1933, as amended, on the basis of the weighted average exercise
price of the options granted under the TomoTherapy Incorporated 2000 Stock Option Plan.</TD>
</TR>

<TR style="font-size: 3pt"><TD>&nbsp;</TD></TR>

<TR valign="top">
    <TD nowrap align="left">(6)</TD>
    <TD>&nbsp;</TD>
    <TD>Represents 6,811,115 shares of Common Stock reserved for issuance upon exercise of
outstanding options granted under the TomoTherapy Incorporated 2002 Stock Option Plan.</TD>
</TR>

<TR style="font-size: 3pt"><TD>&nbsp;</TD></TR>

<TR valign="top">
    <TD nowrap align="left">(7)</TD>
    <TD>&nbsp;</TD>
    <TD>Estimated solely for the purpose of calculating the registration fee pursuant to Rule 457(h)
under the Securities Act of 1933, as amended, on the basis of the weighted average exercise
price of the options granted under the TomoTherapy Incorporated 2002 Stock Option Plan.</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"><!-- Folio -->&nbsp;<!-- /Folio -->
</DIV>

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<DIV style="font-family: 'Times New Roman',Times,serif">








<DIV align="center" style="font-size: 10pt; margin-top: 18pt"><B>PART I</B>
</DIV>


<DIV align="center" style="font-size: 10pt; margin-top: 18pt"><B>INFORMATION REQUIRED IN THE SECTION 10(a) PROSPECTUS</B>
</DIV>


<DIV align="left" style="font-size: 10pt; margin-top: 6pt">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;TomoTherapy Incorporated (&#147;we,&#148; &#147;us,&#148; &#147;our&#148; or the &#147;Company&#148;) are not filing or including in
this Form S-8 the information described in Part&nbsp;I of the Form S-8 (by incorporation by reference
or otherwise) in accordance with the rules and regulations of the Securities and Exchange
Commission (the &#147;Commission&#148;).
</DIV>


<P align="center" style="font-size: 10pt"><!-- Folio -->1<!-- /Folio -->
</DIV>

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<DIV style="font-family: 'Times New Roman',Times,serif">




<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>


<DIV align="left" style="font-size: 10pt; margin-top: 12pt"><B>Item&nbsp;3. </B><U><B>Incorporation of Documents by Reference</B></U>
</DIV>


<DIV align="left" style="font-size: 10pt; margin-top: 6pt">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The Commission allows us to incorporate by reference the information we file with it, which
means that we can disclose important information to you by referring to those documents. The
information incorporated by reference is an important part of this registration statement, and
information that we file later with the Commission will automatically update and supersede this
information. We incorporate by reference the following documents we have filed, or may file, with
the Commission:
</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="4%" style="background: transparent">&nbsp;</TD>
    <TD width="3%" nowrap align="left">(a)</TD>
    <TD width="1%">&nbsp;</TD>
    <TD>The Registration Statement on Form S-1, as amended (File No.
333-140600), and as declared effective on May&nbsp;8, 2007; 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="4%" style="background: transparent">&nbsp;</TD>
    <TD width="3%" nowrap align="left">(b)</TD>
    <TD width="1%">&nbsp;</TD>
    <TD>The description of the Common Stock contained in the Company&#146;s
Registration Statement on Form 8-A filed with the Commission on May&nbsp;8, 2007 (File No.
001-33452), including any subsequently filed amendments and reports updating that
description.</TD>
</TR>

</TABLE>
</DIV>

<DIV align="left" style="font-size: 10pt; margin-top: 6pt">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;In addition, this registration statement will incorporate by reference all documents we file
under Section&nbsp;13(a), 13(c), 14 or 15(d) of the Exchange Act after the date of this registration
statement and before the filing of a post-effective amendment stating that all securities offered
have been sold or deregistering all securities then remaining unsold. All those documents will be
considered a part of this registration statement from the respective dates we file them. A Current
Report on Form 8-K furnished to the Commission will not be incorporated by reference into this
registration statement. Any statement in a document incorporated or deemed to be incorporated by
reference in this registration statement will be deemed to be modified or superseded to the extent
that a statement contained in this registration statement or in any other later filed document that
also is or is deemed to be incorporated by reference modifies or supersedes the statement. Any
statement modified or superseded will not be deemed, except as modified or superseded, to be a part
of this registration statement.
</DIV>


<DIV align="left" style="font-size: 10pt; margin-top: 12pt"><B>Item&nbsp;4. </B><U><B>Description of Securities</B></U>
</DIV>


<DIV align="left" style="font-size: 10pt; margin-top: 6pt">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Not Applicable.
</DIV>


<DIV align="left" style="font-size: 10pt; margin-top: 12pt"><B>Item&nbsp;5. </B><U><B>Interests of Named Experts and Counsel</B></U>
</DIV>


<DIV align="left" style="font-size: 10pt; margin-top: 6pt">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Not Applicable.
</DIV>


<DIV align="left" style="font-size: 10pt; margin-top: 12pt"><B>Item&nbsp;6. </B><U><B>Indemnification of Directors and Officers</B></U>
</DIV>


<DIV align="left" style="font-size: 10pt; margin-top: 6pt">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Our amended and restated articles of incorporation contain provisions that eliminate, to the
maximum extent permitted by the Wisconsin Business Corporation Law, the personal liability of
directors and executive officers for monetary damages for breach of their fiduciary duties as a
director or officer. Our amended and restated articles of incorporation and bylaws provide that we
shall indemnify our directors and executive officers and may indemnify our employees and other
agents to the fullest extent permitted by the Wisconsin Business Corporation Law.
</DIV>


<DIV align="left" style="font-size: 10pt; margin-top: 6pt">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Section&nbsp;180.0851 of the Wisconsin Business Corporation Law requires us to indemnify a director
or officer, to the extent such person is successful on the merits or otherwise in the defense of a
proceeding for all reasonable expenses incurred in the proceeding, if such person was a party to
such proceeding because he or she was our director or officer unless it is determined that he or
she breached or failed to perform a duty owed to us and such breach or failure to perform
constitutes: (i)&nbsp;a willful failure to deal fairly with us or our shareholders in connection with a
matter in which the director or officer has a material conflict of interest, (ii)&nbsp;a violation of
criminal law, unless the director or officer had reasonable cause to believe his or her conduct was
unlawful, (iii)&nbsp;a transaction from which the director or officer derived an improper personal
profit or (iv)&nbsp;willful misconduct.
</DIV>


<P align="center" style="font-size: 10pt"><!-- Folio -->II-1<!-- /Folio -->
</DIV>

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<DIV style="font-family: 'Times New Roman',Times,serif">




<DIV align="left" style="font-size: 10pt; margin-top: 6pt">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Section&nbsp;180.0858 of the Wisconsin Business Corporation Law provides that subject to
certain limitations, the mandatory indemnification provisions do not preclude any additional right
to indemnification or allowance of expenses that a director or officer may have under the articles
of incorporation or bylaws of the Registrant, a written agreement between the director or officer
and us or a resolution of the Board of Directors or the shareholders.
</DIV>


<DIV align="left" style="font-size: 10pt; margin-top: 6pt">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Unless otherwise provided in our amended and restated articles of incorporation or bylaws, or
by written agreement between our director or officer and us, an officer or director seeking
indemnification is entitled to indemnification if approved in any of the following manners as
specified in Section&nbsp;180.0855 of the Wisconsin Business Corporation Law:
</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">(i)</TD>
    <TD width="1%">&nbsp;</TD>
    <TD>by majority vote of a disinterested quorum of the Board of Directors,</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">(ii)</TD>
    <TD width="1%">&nbsp;</TD>
    <TD>by independent legal counsel chosen by a quorum of disinterested directors or its committee,</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">(iii)</TD>
    <TD width="1%">&nbsp;</TD>
    <TD>by a panel of three arbitrators (one of which is chosen by a quorum of disinterested directors),</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">(iv)</TD>
    <TD width="1%">&nbsp;</TD>
    <TD>by the vote of the shareholders,</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">(v)</TD>
    <TD width="1%">&nbsp;</TD>
    <TD>by a court; or</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">(vi)</TD>
    <TD width="1%">&nbsp;</TD>
    <TD>by any other method permitted in Section&nbsp;180.0858 of the Wisconsin Business Corporation
Law.</TD>
</TR>

</TABLE>
</DIV>

<DIV align="left" style="font-size: 10pt; margin-top: 6pt">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Reasonable expenses incurred by a director or officer who is a party to a proceeding may be
reimbursed by the Registrant, pursuant to Section&nbsp;180.0853 of the Wisconsin Business Corporation
Law, at such time as the director or officer furnishes to the corporation written affirmation of
his good faith that he has not breached or failed to perform his duties; and written confirmation
to repay any amounts advanced if it is determined that indemnification by us is not required.
</DIV>

<DIV align="left" style="font-size: 10pt; margin-top: 6pt">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Section&nbsp;180.0859 of the Wisconsin Business Corporation Law provides that it is the public
policy of the State of Wisconsin to require or permit indemnification, allowance of expenses and
insurance to the extent required or permitted under Sections&nbsp;180.0850 to 180.0858 of the Wisconsin
Business Corporation Law for any liability incurred in connection with a proceeding involving a
federal or state statute, rule or regulation regulating the offer, sale or purchase of securities.
</DIV>

<DIV align="left" style="font-size: 10pt; margin-top: 6pt">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Under Section&nbsp;180.0828 of the Wisconsin Business Corporation Law, our directors are not
personally liable for breach of any duty resulting solely from his or her status as a director,
unless it shall be proved that the director&#146;s conduct constituted conduct described in the first
paragraph of this item.
</DIV>


<DIV align="left" style="font-size: 10pt; margin-top: 6pt">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;In addition, we maintain directors&#146; and officers&#146; liability insurance that insures against
certain liabilities, including liabilities under the Securities Act, subject to applicable
restrictions.
</DIV>

<DIV align="left" style="font-size: 10pt; margin-top: 12pt"><B>Item&nbsp;7. </B><U><B>Exemption From Registration Claimed</B></U>
</DIV>


<DIV align="left" style="font-size: 10pt; margin-top: 6pt">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Not applicable.
</DIV>


<DIV align="left" style="font-size: 10pt; margin-top: 12pt"><B>Item&nbsp;8. </B><U><B>Exhibits</B></U>
</DIV>


<DIV align="left" style="font-size: 10pt; margin-top: 6pt">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;See Index to Exhibits on page II-5.
</DIV>


<DIV align="left" style="font-size: 10pt; margin-top: 12pt"><B>Item&nbsp;9. </B><U><B>Undertakings</B></U>
</DIV>


<DIV align="left" style="font-size: 10pt; margin-top: 6pt">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;(a)&nbsp;We hereby undertake:
</DIV>



<DIV align="left" style="font-size: 10pt; margin-top: 6pt; margin-left: 2%">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;(1) To file, during any period in which offers or sales are being made, a post-effective
amendment to this registration statement:
</DIV>

<P align="center" style="font-size: 10pt"><!-- Folio -->II-2<!-- /Folio -->
</DIV>

<!-- PAGEBREAK -->
<P><HR noshade><P>
<H5 align="left" style="page-break-before:always">&nbsp;</H5><P>

<DIV style="font-family: 'Times New Roman',Times,serif">

<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="8%" style="background: transparent">&nbsp;</TD>
    <TD width="3%" nowrap align="left">(i)</TD>
    <TD width="1%">&nbsp;</TD>
    <TD>to include any prospectus required
by Section&nbsp;10(a)(3) of the Securities Act;</TD>
</TR>

<TR>
    <TD style="font-size: 6pt">&nbsp;</TD>
</TR><TR valign="top" style="font-size: 10pt; color: #000000; background: transparent">
    <TD width="8%" style="background: transparent">&nbsp;</TD>
    <TD width="3%" nowrap align="left">(ii)</TD>
    <TD width="1%">&nbsp;</TD>
    <TD>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
the registration statement. Notwithstanding the matters stated above, any
increase or decrease in volume of securities offered (if the total dollar value
of securities offered would not exceed the value we 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 in accordance
with 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; 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="8%" style="background: transparent">&nbsp;</TD>
    <TD width="3%" nowrap align="left">(iii)</TD>
    <TD width="1%">&nbsp;</TD>
    <TD>to include any material information
with respect to the plan of distribution not previously disclosed in the
registration statement or any material change to that information in the
registration statement;</TD>
</TR>

</TABLE>
</DIV>


<DIV align="left" style="font-size: 10pt; margin-top: 6pt; margin-left: 2%"><I>provided, however</I>, that paragraphs (a)(1)(i) and (a)(1)(ii) do not apply if the information
required to be included in a post-effective amendment by those paragraphs is contained in
reports filed with or furnished to the Commission by the registrant in accordance with Section
13 or Section 15(d) of the Exchange Act that are incorporated by reference in the registration
statement.
</DIV>


<DIV align="left" style="font-size: 10pt; margin-top: 6pt; margin-left: 2%">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;(2) That, for the purpose of determining any liability under the Securities Act, each
post-effective amendment will be deemed to be a new registration statement relating to the
offered securities, and the offering of the securities at that time will be deemed to be the
initial bona fide offering thereof.
</DIV>


<DIV align="left" style="font-size: 10pt; margin-top: 6pt; margin-left: 2%">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;(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.
</DIV>

<DIV align="left" style="font-size: 10pt; margin-top: 6pt">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;(b)&nbsp;We hereby undertake that, for purposes of determining any liability under the Securities
Act, each filing of our annual report under Section 13(a) or Section 15(d) of the Exchange Act
(and, where applicable, each filing of an employee benefit plan&#146;s annual report under Section 15(d)
of the Exchange Act) that is incorporated by reference in the registration statement will be deemed
to be a new registration statement relating to the offered securities, and the offering of
securities at that time will be deemed to be the initial bona fide offering thereof.
</DIV>


<DIV align="left" style="font-size: 10pt; margin-top: 6pt">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;(c)&nbsp;To the extent that indemnification for liabilities arising under the Securities Act may be
permitted to directors, officers and controlling persons of the registrant in accordance with the
provisions mentioned above, or otherwise, we have been advised that in the opinion of the
Commission indemnification under those circumstances is against public policy as expressed in the
Securities Act and is, therefore, unenforceable. In the event that a claim for indemnification
against those 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 the 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 indemnification by it is against public policy as expressed in
the Securities Act and will be governed by the final adjudication of the issue.
</DIV>


<P align="center" style="font-size: 10pt"><!-- Folio -->II-3<!-- /Folio -->
</DIV>

<!-- PAGEBREAK -->
<P><HR noshade><P>
<H5 align="left" style="page-break-before:always">&nbsp;</H5><P>

<DIV style="font-family: 'Times New Roman',Times,serif">




<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, as amended, we have duly
caused this to the Registration Statement on Form S-8 to be signed on its behalf by the
undersigned, thereunto duly authorized, in the City of Madison, State
of Wisconsin, on the 10th day
of May&nbsp;2007.
</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"><B>TOMOTHERAPY INCORPORATED</B> <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/ Frederick A. Robertson
&nbsp;</TD>
    <TD>&nbsp;</TD>
</TR><TR>
    <TD align="left">&nbsp;</TD>
    <TD>&nbsp;</TD>
    <TD colspan="2" align="left">Frederick A. Robertson, M.D.     &nbsp;</TD>
    <TD>&nbsp;</TD>
</TR><TR>
    <TD align="left">&nbsp;</TD>
    <TD>&nbsp;</TD>
    <TD colspan="2" align="left"><I>Chief Executive Officer</I>&nbsp;</TD>
    <TD>&nbsp;</TD>
</TR>
<TR>
    <TD colspan="5">&nbsp;</TD>
</TR>
</TABLE>

<DIV align="center" style="font-size: 10pt; margin-top: 18pt"><B>POWER OF ATTORNEY</B>
</DIV>



<DIV align="left" style="font-size: 10pt; margin-top: 6pt">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;KNOW ALL MEN BY THESE PRESENTS, that each person whose signature appears below
constitutes and appoints Stephen C. Hathaway and Shawn D. Guse his true and lawful
attorney-in-fact, with full power of substitution and resubstitution for him and in his name, place
and stead, in any and all capacities to sign any and all amendments including post-effective
amendments to this registration statement, and to file the same, with all exhibits thereto, and
other documents in connection therewith, with the SEC, hereby ratifying and confirming all that
said attorney-in-fact or his substitute, each acting alone, may lawfully do or cause to be done by
virtue thereof.
</DIV>

<DIV align="left" style="font-size: 10pt; margin-top: 6pt">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Pursuant to the requirements of the Securities Act, this Registration Statement has been
signed by the following persons in the capacities and on the dates indicated.
</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="40%">&nbsp;</TD>
    <TD width="5%">&nbsp;</TD>
    <TD width="35%">&nbsp;</TD>
    <TD width="5%">&nbsp;</TD>
    <TD width="15%">&nbsp;</TD>
</TR>
<TR style="font-size: 8pt" valign="bottom">
    <TD nowrap align="center" style="border-bottom: 1px solid #000000"><B>Signature</B></TD>
    <TD>&nbsp;</TD>
    <TD nowrap align="center" style="border-bottom: 1px solid #000000"><B>Position</B></TD>
    <TD>&nbsp;</TD>
    <TD nowrap align="center" style="border-bottom: 1px solid #000000"><B>Date</B></TD>
</TR>

<!-- End Table Head -->
<!-- Begin Table Body -->
<TR valign="bottom"><!-- Blank Space -->
    <TD align="right">&nbsp;</TD>
    <TD>&nbsp;</TD>
    <TD align="center" valign="top">&nbsp;</TD>
    <TD>&nbsp;</TD>
    <TD align="center" valign="top">&nbsp;</TD>
</TR>
<TR valign="top" style="padding-top: 1em">
    <TD align="left" valign="top">/s/ Frederick A. Robertson, M.D.
<DIV style="font-size: 1pt; border-bottom: 1px solid #000000">&nbsp;</DIV>
Frederick A. Robertson, M.D.</TD>
    <TD>&nbsp;</TD>
    <TD align="center">
Chief Executive Officer and
Director<BR>(principal executive
officer)
</TD>
    <TD>&nbsp;</TD>
    <TD align="center" valign="top">May&nbsp;10, 2007</TD>
</TR>
<TR valign="top" style="padding-top: 1em">
    <TD align="left" valign="top">&nbsp;
<DIV style="font-size: 1pt; border-bottom: 1px solid #000000">&nbsp;</DIV>
Paul J. Reckwerdt</TD>
    <TD>&nbsp;</TD>
    <TD align="center">
President and Director
</TD>
    <TD>&nbsp;</TD>
    <TD align="center" valign="top">May&nbsp;10, 2007</TD>
</TR>
<TR valign="top" style="padding-top: 1em">
    <TD align="left" valign="top">/s/  Stephen C. Hathaway
<DIV style="font-size: 1pt; border-bottom: 1px solid #000000">&nbsp;</DIV>
Stephen C. Hathaway</TD>
    <TD>&nbsp;</TD>
    <TD align="center">
Chief Financial Officer<BR>
(principal  financial and
accounting officer)
</TD>
    <TD>&nbsp;</TD>
    <TD align="center" valign="top">May&nbsp;10, 2007</TD>
</TR>
<TR valign="top" style="padding-top: 1em">
    <TD align="left" valign="top">/s/ T. Rockwell Mackie, Ph.D.
<DIV style="font-size: 1pt; border-bottom: 1px solid #000000">&nbsp;</DIV>
T. Rockwell Mackie, Ph.D.</TD>
    <TD>&nbsp;</TD>
    <TD align="center">
Director
</TD>
    <TD>&nbsp;</TD>
    <TD align="center" valign="top">May&nbsp;10, 2007</TD>
</TR>
<TR valign="top" style="padding-top: 1em">
    <TD align="left" valign="top">&nbsp;
<DIV style="font-size: 1pt; border-bottom: 1px solid #000000">&nbsp;</DIV>
Michael J. Cudahy</TD>
    <TD>&nbsp;</TD>
    <TD align="center">
Director
</TD>
    <TD>&nbsp;</TD>
    <TD align="center" valign="top">May&nbsp;10, 2007</TD>
</TR>
<TR valign="top" style="padding-top: 1em">
    <TD align="left" valign="top">/s/ John J. McDonough
<DIV style="font-size: 1pt; border-bottom: 1px solid #000000">&nbsp;</DIV>
John J. McDonough</TD>
    <TD>&nbsp;</TD>
    <TD align="center">
Director
</TD>
    <TD>&nbsp;</TD>
    <TD align="center" valign="top">May&nbsp;10, 2007</TD>
</TR>
<TR valign="top" style="padding-top: 1em">
    <TD align="left" valign="top">/s/ John Neis
<DIV style="font-size: 1pt; border-bottom: 1px solid #000000">&nbsp;</DIV>
John Neis</TD>
    <TD>&nbsp;</TD>
    <TD align="center">
Director
</TD>
    <TD>&nbsp;</TD>
    <TD align="center" valign="top">May&nbsp;10, 2007</TD>
</TR>
<TR valign="top" style="padding-top: 1em">
    <TD align="left" valign="top">/s/ Cary J. Nolan
<DIV style="font-size: 1pt; border-bottom: 1px solid #000000">&nbsp;</DIV>
Cary J. Nolan</TD>
    <TD>&nbsp;</TD>
    <TD align="center">
Director
</TD>
    <TD>&nbsp;</TD>
    <TD align="center" valign="top">May&nbsp;10, 2007</TD>
</TR>
<TR valign="top" style="padding-top: 1em">
    <TD align="left" valign="top">&nbsp;
<DIV style="font-size: 1pt; border-bottom: 1px solid #000000">&nbsp;</DIV>
Carlos A. Perez, M.D.</TD>
    <TD>&nbsp;</TD>
    <TD align="center">
Director
</TD>
    <TD>&nbsp;</TD>
    <TD align="center" valign="top">May&nbsp;10, 2007</TD>
</TR>
<TR valign="top" style="padding-top: 1em">
    <TD align="left" valign="top">&nbsp;
<DIV style="font-size: 1pt; border-bottom: 1px solid #000000">&nbsp;</DIV>
Sam R. Leno</TD>
    <TD>&nbsp;</TD>
    <TD align="center">
Director
</TD>
    <TD>&nbsp;</TD>
    <TD align="center" valign="top">May&nbsp;10, 2007</TD>
</TR>
<TR valign="top" style="padding-top: 1em">
    <TD align="left" valign="top">/s/ Frances S. Taylor
<DIV style="font-size: 1pt; border-bottom: 1px solid #000000">&nbsp;</DIV>
Frances S. Taylor</TD>
    <TD>&nbsp;</TD>
    <TD align="center">
Director
</TD>
    <TD>&nbsp;</TD>
    <TD align="center" valign="top">May&nbsp;10, 2007</TD>
</TR>
<!-- End Table Body -->
</TABLE>
</DIV>


<P align="center" style="font-size: 10pt"><!-- Folio -->II-4<!-- /Folio -->
</DIV>

<!-- PAGEBREAK -->
<P><HR noshade><P>
<H5 align="left" style="page-break-before:always">&nbsp;</H5><P>

<DIV style="font-family: 'Times New Roman',Times,serif">


<DIV align="center" style="font-size: 10pt; margin-top: 18pt"><B>INDEX TO EXHIBITS</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="5%">&nbsp;</TD>
    <TD width="5%">&nbsp;</TD>
    <TD width="90%">&nbsp;</TD>
</TR>
<TR style="font-size: 8pt" valign="bottom">
    <TD nowrap align="left" style="border-bottom: 1px solid #000000"><B>EXHIBIT</B></TD>
    <TD>&nbsp;</TD>
    <TD>&nbsp;</TD>
</TR>

<!-- End Table Head -->
<!-- Begin Table Body -->
<TR valign="bottom"><!-- Blank Space -->
    <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">4.1
</DIV></TD>
    <TD>&nbsp;</TD>
    <TD align="left" valign="top">Amended and Restated Articles of Incorporation (incorporated by reference to
Exhibit&nbsp;3.2 of Amendment No. 3 to the Company&#146;s Registration Statement on
Form&nbsp;S-1(No.&nbsp;333-140600) filed on April 19, 2007).</TD>
</TR>
<TR valign="bottom"><!-- Blank Space -->
    <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">Amended and Restated Bylaws (incorporated by reference to Exhibit&nbsp;3.4 of
Amendment No. 2 to the Company&#146;s Registration Statement on Form&nbsp;S-1 (No.
333-140600) filed on April 16, 2007)</TD>
</TR>
<TR valign="bottom"><!-- Blank Space -->
    <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">Amended and Restated Investment Rights Agreement, dated February&nbsp;8, 2007, by and
among the TomoTherapy Incorporated and the other parties thereto (incorporated by
reference to Exhibit&nbsp;10.1 of Amendment No. 1 to the Company&#146;s
Registration Statement on Form&nbsp;S-1 (No.&nbsp;333-140600) filed
on March 22, 2007)</TD>
</TR>
<TR valign="bottom"><!-- Blank Space -->
    <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 Michael Best &#038; Friedrich LLP</TD>
</TR>
<TR valign="bottom"><!-- Blank Space -->
    <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">10.1
</DIV></TD>
    <TD>&nbsp;</TD>
    <TD align="left" valign="top">TomoTherapy Incorporated Incentive Stock Option Plan and forms of agreements
relating thereto (incorporated by reference to Exhibit&nbsp;10.16 to the Company&#146;s
Registration Statement on Form&nbsp;S-1 (No.&nbsp;333-140600) filed on February&nbsp;12, 2007)</TD>
</TR>
<TR valign="bottom"><!-- Blank Space -->
    <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">10.2
</DIV></TD>
    <TD>&nbsp;</TD>
    <TD align="left" valign="top">TomoTherapy Incorporated 2000 Stock Option Plan (incorporated by reference to
Exhibit&nbsp;10.17 to the Company&#146;s Registration Statement on Form&nbsp;S-1 (No.
333-140600) filed on February&nbsp;12, 2007)</TD>
</TR>
<TR valign="bottom"><!-- Blank Space -->
    <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">10.3
</DIV></TD>
    <TD>&nbsp;</TD>
    <TD align="left" valign="top">TomoTherapy Incorporated 2002 Stock Option Plan (incorporated by reference
to Exhibit&nbsp;10.18 to the Company&#146;s Registration Statement on Form&nbsp;S-1 (No.
333-140600) filed on February&nbsp;12, 2007)</TD>
</TR>
<TR valign="bottom"><!-- Blank Space -->
    <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 Michael Best &#038; Friedrich LLP (included in Exhibit&nbsp;5.1)</TD>
</TR>
<TR valign="bottom"><!-- Blank Space -->
    <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 Grant Thornton LLP, independent registered public accounting firm</TD>
</TR>
<TR valign="bottom"><!-- Blank Space -->
    <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">23.3
</DIV></TD>
    <TD>&nbsp;</TD>
    <TD align="left" valign="top">Consent of Virchow Krause Valuation, LLC</TD>
</TR>
<TR valign="bottom"><!-- Blank Space -->
    <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 (see page II-4)</TD>
</TR>
<!-- End Table Body -->
</TABLE>
</DIV>



<P align="center" style="font-size: 10pt"><!-- Folio -->II-5<!-- /Folio -->
</DIV>

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{"company-data": {"conformed-name": "TomoTherapy Inc", "cik": "0001317872", "assigned-sic": "3845", "irs-number": "000000000"}, "filing-values": {"form-type": "S-8", "act": "33", "file-number": "333-142829", "film-number": "07839083"}, "business-address": {"street1": "1240 DEMING WAY", "city": "MADISON", "state": "WI", "zip": "53717-1954"}, "mail-address": {"street1": "1240 DEMING WAY", "city": "MADISON", "state": "WI", "zip": "53717-1954"}}
sv8
As
filed with the Securities and Exchange Commission on May 10, 2007
Registration No. 333
SECURITIES AND EXCHANGE COMMISSION
WASHINGTON, D.C. 20549
FORM S-8
REGISTRATION STATEMENT
UNDER
THE SECURITIES ACT OF 1933
TOMOTHERAPY INCORPORATED
(Exact name of registrant as specified in its charter)
Wisconsin
(State or Other Jurisdiction of
Incorporation or Organization)
39-1914727
(I.R.S. Employer
Identification Number)
1240 Deming Way
Madison, Wisconsin 53717
(Address of Principal Executive Offices including Zip Code)
TomoTherapy Incorporated Incentive Stock Option Plan
TomoTherapy Incorporated 2000 Stock Option Plan
Tomotherapy Incorporated 2002 Stock Option Plan
(Full Title of the Plan)
Stephen C. Hathaway
Copy to:
Chief Financial Officer and Treasurer
TomoTherapy Incorporated
1240 Deming Way
Madison, Wisconsin 53717
(608) 824-2800
Geoffrey R. Morgan, Esq.
Michael Best & Friedrich, LLP
100 East Wisconsin Avenue
Milwaukee, Wisconsin 53202
(414) 225-2752
(Name and Address, Including Zip Code, and Telephone Number,
Including Area Code, of Agent for Service)
CALCULATION OF REGISTRATION FEE
Proposed
Proposed
Maximum
Maximum
Title Of
Amount
Offering
Aggregate
Amount Of
Securities To Be
To Be
Price Per
Offering
Registration
Registered
Registered(1)
Share
Price
Fee
Common Stock,
par value $0.01 per
share
73,304
(2)
$0.11(3)
$22,725
$.25
Common Stock,
par value $0.01 per
share
113,424
(4)
$0.31(5)
$35,162
$1.08
Common Stock, par
value $0.01 per
share
6,811,115
(6)
$4.19(7)
$28,538,572
$877.50
(1)
This Registration Statement shall also cover any additional shares of Common Stock
which become issuable under any of the plans being registered pursuant to this Registration
Statement by reason of any stock dividend, stock split, recapitalization or any other similar
transaction effected without the receipt of consideration which results in an increase in the
number of the Registrant's outstanding shares of Common Stock.
(2)
Represents 73,304 shares of Common Stock reserved for issuance upon exercise of outstanding
options granted under the TomoTherapy Incentive Stock Option Plan.
(3)
Estimated solely for the purpose of calculating the registration fee pursuant to Rule 457(h)
under the Securities Act of 1933, as amended, on the basis of the weighted average exercise
price of the options granted under the TomoTherapy Incorporated Incentive Stock Option Plan.
(4)
Represents 113,424 shares of Common Stock reserved for issuance upon exercise of outstanding
options granted under the TomoTherapy Incorporated 2000 Stock Option Plan.
(5)
Estimated solely for the purpose of calculating the registration fee pursuant to Rule 457(h)
under the Securities Act of 1933, as amended, on the basis of the weighted average exercise
price of the options granted under the TomoTherapy Incorporated 2000 Stock Option Plan.
(6)
Represents 6,811,115 shares of Common Stock reserved for issuance upon exercise of
outstanding options granted under the TomoTherapy Incorporated 2002 Stock Option Plan.
(7)
Estimated solely for the purpose of calculating the registration fee pursuant to Rule 457(h)
under the Securities Act of 1933, as amended, on the basis of the weighted average exercise
price of the options granted under the TomoTherapy Incorporated 2002 Stock Option Plan.
PART I
INFORMATION REQUIRED IN THE SECTION 10(a) PROSPECTUS
TomoTherapy Incorporated ("we," "us," "our" or the "Company") are not filing or including in
this Form S-8 the information described in Part I of the Form S-8 (by incorporation by reference
or otherwise) in accordance with the rules and regulations of the Securities and Exchange
Commission (the "Commission").
1
PART II
INFORMATION REQUIRED IN THE REGISTRATION STATEMENT
Item 3.
Incorporation of Documents by Reference
The Commission allows us to incorporate by reference the information we file with it, which
means that we can disclose important information to you by referring to those documents. The
information incorporated by reference is an important part of this registration statement, and
information that we file later with the Commission will automatically update and supersede this
information. We incorporate by reference the following documents we have filed, or may file, with
the Commission:
(a)
The Registration Statement on Form S-1, as amended (File No.
333-140600), and as declared effective on May 8, 2007; and
(b)
The description of the Common Stock contained in the Company's
Registration Statement on Form 8-A filed with the Commission on May 8, 2007 (File No.
001-33452), including any subsequently filed amendments and reports updating that
description.
In addition, this registration statement will incorporate by reference all documents we file
under Section 13(a), 13(c), 14 or 15(d) of the Exchange Act after the date of this registration
statement and before the filing of a post-effective amendment stating that all securities offered
have been sold or deregistering all securities then remaining unsold. All those documents will be
considered a part of this registration statement from the respective dates we file them. A Current
Report on Form 8-K furnished to the Commission will not be incorporated by reference into this
registration statement. Any statement in a document incorporated or deemed to be incorporated by
reference in this registration statement will be deemed to be modified or superseded to the extent
that a statement contained in this registration statement or in any other later filed document that
also is or is deemed to be incorporated by reference modifies or supersedes the statement. Any
statement modified or superseded will not be deemed, except as modified or superseded, to be 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
Our amended and restated articles of incorporation contain provisions that eliminate, to the
maximum extent permitted by the Wisconsin Business Corporation Law, the personal liability of
directors and executive officers for monetary damages for breach of their fiduciary duties as a
director or officer. Our amended and restated articles of incorporation and bylaws provide that we
shall indemnify our directors and executive officers and may indemnify our employees and other
agents to the fullest extent permitted by the Wisconsin Business Corporation Law.
Section 180.0851 of the Wisconsin Business Corporation Law requires us to indemnify a director
or officer, to the extent such person is successful on the merits or otherwise in the defense of a
proceeding for all reasonable expenses incurred in the proceeding, if such person was a party to
such proceeding because he or she was our director or officer unless it is determined that he or
she breached or failed to perform a duty owed to us and such breach or failure to perform
constitutes: (i) a willful failure to deal fairly with us or our shareholders in connection with a
matter in which the director or officer has a material conflict of interest, (ii) a violation of
criminal law, unless the director or officer had reasonable cause to believe his or her conduct was
unlawful, (iii) a transaction from which the director or officer derived an improper personal
profit or (iv) willful misconduct.
II-1
Section 180.0858 of the Wisconsin Business Corporation Law provides that subject to
certain limitations, the mandatory indemnification provisions do not preclude any additional right
to indemnification or allowance of expenses that a director or officer may have under the articles
of incorporation or bylaws of the Registrant, a written agreement between the director or officer
and us or a resolution of the Board of Directors or the shareholders.
Unless otherwise provided in our amended and restated articles of incorporation or bylaws, or
by written agreement between our director or officer and us, an officer or director seeking
indemnification is entitled to indemnification if approved in any of the following manners as
specified in Section 180.0855 of the Wisconsin Business Corporation Law:
(i)
by majority vote of a disinterested quorum of the Board of Directors,
(ii)
by independent legal counsel chosen by a quorum of disinterested directors or its committee,
(iii)
by a panel of three arbitrators (one of which is chosen by a quorum of disinterested directors),
(iv)
by the vote of the shareholders,
(v)
by a court; or
(vi)
by any other method permitted in Section 180.0858 of the Wisconsin Business Corporation
Law.
Reasonable expenses incurred by a director or officer who is a party to a proceeding may be
reimbursed by the Registrant, pursuant to Section 180.0853 of the Wisconsin Business Corporation
Law, at such time as the director or officer furnishes to the corporation written affirmation of
his good faith that he has not breached or failed to perform his duties; and written confirmation
to repay any amounts advanced if it is determined that indemnification by us is not required.
Section 180.0859 of the Wisconsin Business Corporation Law provides that it is the public
policy of the State of Wisconsin to require or permit indemnification, allowance of expenses and
insurance to the extent required or permitted under Sections 180.0850 to 180.0858 of the Wisconsin
Business Corporation Law for any liability incurred in connection with a proceeding involving a
federal or state statute, rule or regulation regulating the offer, sale or purchase of securities.
Under Section 180.0828 of the Wisconsin Business Corporation Law, our directors are not
personally liable for breach of any duty resulting solely from his or her status as a director,
unless it shall be proved that the director's conduct constituted conduct described in the first
paragraph of this item.
In addition, we maintain directors' and officers' liability insurance that insures against
certain liabilities, including liabilities under the Securities Act, subject to applicable
restrictions.
Item 7.
Exemption From Registration Claimed
Not applicable.
Item 8.
Exhibits
See Index to Exhibits on page II-5.
Item 9.
Undertakings
(a) We hereby undertake:
(1) To file, during any period in which offers or sales are being made, a post-effective
amendment to this registration statement:
II-2
(i)
to include any prospectus required
by Section 10(a)(3) of the Securities 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
the registration statement. Notwithstanding the matters stated above, any
increase or decrease in volume of securities offered (if the total dollar value
of securities offered would not exceed the value we 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 in accordance
with 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; and
(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 that information in the
registration statement;
provided, however
, that paragraphs (a)(1)(i) and (a)(1)(ii) do not apply if the information
required to be included in a post-effective amendment by those paragraphs is contained in
reports filed with or furnished to the Commission by the registrant in accordance with Section
13 or Section 15(d) of the Exchange Act that are incorporated by reference in the registration
statement.
(2) That, for the purpose of determining any liability under the Securities Act, each
post-effective amendment will be deemed to be a new registration statement relating to the
offered securities, and the offering of the securities at that time will 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) We hereby undertake that, for purposes of determining any liability under the Securities
Act, each filing of our annual report under Section 13(a) or Section 15(d) of the Exchange Act
(and, where applicable, each filing of an employee benefit plan's annual report under Section 15(d)
of the Exchange Act) that is incorporated by reference in the registration statement will be deemed
to be a new registration statement relating to the offered securities, and the offering of
securities at that time will be deemed to be the initial bona fide offering thereof.
(c) To the extent that indemnification for liabilities arising under the Securities Act may be
permitted to directors, officers and controlling persons of the registrant in accordance with the
provisions mentioned above, or otherwise, we have been advised that in the opinion of the
Commission indemnification under those circumstances is against public policy as expressed in the
Securities Act and is, therefore, unenforceable. In the event that a claim for indemnification
against those 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 the 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 indemnification by it is against public policy as expressed in
the Securities Act and will be governed by the final adjudication of the issue.
II-3
SIGNATURES
Pursuant to the requirements of the Securities Act of 1933, as amended, we have duly
caused this to the Registration Statement on Form S-8 to be signed on its behalf by the
undersigned, thereunto duly authorized, in the City of Madison, State
of Wisconsin, on the 10th day
of May 2007.
TOMOTHERAPY INCORPORATED
By:
/s/ Frederick A. Robertson
Frederick A. Robertson, M.D.
Chief Executive Officer
POWER OF ATTORNEY
KNOW ALL MEN BY THESE PRESENTS, that each person whose signature appears below
constitutes and appoints Stephen C. Hathaway and Shawn D. Guse his true and lawful
attorney-in-fact, with full power of substitution and resubstitution for him and in his name, place
and stead, in any and all capacities to sign any and all amendments including post-effective
amendments to this registration statement, and to file the same, with all exhibits thereto, and
other documents in connection therewith, with the SEC, hereby ratifying and confirming all that
said attorney-in-fact or his substitute, each acting alone, may lawfully do or cause to be done by
virtue thereof.
Pursuant to the requirements of the Securities Act, this Registration Statement has been
signed by the following persons in the capacities and on the dates indicated.
Signature
Position
Date
/s/ Frederick A. Robertson, M.D.
Frederick A. Robertson, M.D.
Chief Executive Officer and
Director
(principal executive
officer)
May 10, 2007
Paul J. Reckwerdt
President and Director
May 10, 2007
/s/  Stephen C. Hathaway
Stephen C. Hathaway
Chief Financial Officer
(principal  financial and
accounting officer)
May 10, 2007
/s/ T. Rockwell Mackie, Ph.D.
T. Rockwell Mackie, Ph.D.
Director
May 10, 2007
Michael J. Cudahy
Director
May 10, 2007
/s/ John J. McDonough
John J. McDonough
Director
May 10, 2007
/s/ John Neis
John Neis
Director
May 10, 2007
/s/ Cary J. Nolan
Cary J. Nolan
Director
May 10, 2007
Carlos A. Perez, M.D.
Director
May 10, 2007
Sam R. Leno
Director
May 10, 2007
/s/ Frances S. Taylor
Frances S. Taylor
Director
May 10, 2007
II-4
INDEX TO EXHIBITS
EXHIBIT
4.1
Amended and Restated Articles of Incorporation (incorporated by reference to
Exhibit 3.2 of Amendment No. 3 to the Company's Registration Statement on
Form S-1(No. 333-140600) filed on April 19, 2007).
4.2
Amended and Restated Bylaws (incorporated by reference to Exhibit 3.4 of
Amendment No. 2 to the Company's Registration Statement on Form S-1 (No.
333-140600) filed on April 16, 2007)
4.3
Amended and Restated Investment Rights Agreement, dated February 8, 2007, by and
among the TomoTherapy Incorporated and the other parties thereto (incorporated by
reference to Exhibit 10.1 of Amendment No. 1 to the Company's
Registration Statement on Form S-1 (No. 333-140600) filed
on March 22, 2007)
5.1
Opinion of Michael Best & Friedrich LLP
10.1
TomoTherapy Incorporated Incentive Stock Option Plan and forms of agreements
relating thereto (incorporated by reference to Exhibit 10.16 to the Company's
Registration Statement on Form S-1 (No. 333-140600) filed on February 12, 2007)
10.2
TomoTherapy Incorporated 2000 Stock Option Plan (incorporated by reference to
Exhibit 10.17 to the Company's Registration Statement on Form S-1 (No.
333-140600) filed on February 12, 2007)
10.3
TomoTherapy Incorporated 2002 Stock Option Plan (incorporated by reference
to Exhibit 10.18 to the Company's Registration Statement on Form S-1 (No.
333-140600) filed on February 12, 2007)
23.1
Consent of Michael Best & Friedrich LLP (included in Exhibit 5.1)
23.2
Consent of Grant Thornton LLP, independent registered public accounting firm
23.3
Consent of Virchow Krause Valuation, LLC
24.1
Power of Attorney (see page II-4)
II-5