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<P align="center" style="font-size: 14pt"><B>UNITED STATES<BR>
SECURITIES AND EXCHANGE COMMISSION<BR>
<FONT style="font-size: 12pt">Washington, D.C. 20549
</FONT></B>

<P align="center" style="font-size: 18pt"><B>FORM 8-K</B>

<P align="center" style="font-size: 12pt"><B>CURRENT REPORT<BR>
Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934</B>

<P align="center" style="font-size: 10pt"><B>Date of Report (Date of earliest event reported): April 15, 2009</B>

<P align="center">

<P align="center" style="font-size: 24pt"><B>TOMOTHERAPY INCORPORATED<BR></B>
<FONT style="font-size: 10pt">(Exact name of registrant as specified in its charter)
</FONT>

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    <TD width="32%">&nbsp;</TD>
    <TD width="1%">&nbsp;</TD>
    <TD width="33%">&nbsp;</TD>
    <TD width="1%">&nbsp;</TD>
    <TD width="32%">&nbsp;</TD>
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<TR valign="bottom">
    <TD style="border-bottom: 1px solid #000000"><B>Wisconsin</B></TD>
    <TD>&nbsp;</TD>
    <TD style="border-bottom: 1px solid #000000"><B>001-33452</B></TD>
    <TD>&nbsp;</TD>
    <TD style="border-bottom: 1px solid #000000"><B>39-1914727</B></TD>
</TR>
<TR valign="top">
    <TD>(State or other Jurisdiction of Incorporation)</TD>
    <TD>&nbsp;</TD>
    <TD>(Commission File Number)</TD>
    <TD>&nbsp;</TD>
    <TD>(IRS Employer Identification No.)</TD>
</TR>
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    <TD width="49%">&nbsp;</TD>
    <TD width="1%">&nbsp;</TD>
    <TD width="49%">&nbsp;</TD>
</TR>
<TR valign="bottom">
    <TD style="border-bottom: 1px solid #000000"><B>1240 Deming Way<BR>Madison, Wisconsin<BR></B></TD>
    <TD>&nbsp;</TD>
    <TD style="border-bottom: 1px solid #000000"><B>53717</B></TD>
</TR>
<TR valign="top">
    <TD>(Address of Principal Executive Offices)</TD>
    <TD>&nbsp;</TD>
    <TD>(Zip Code)</TD>
</TR>
</TABLE>

<P align="center" style="font-size: 10pt">Registrant&#146;s telephone number, including area code: <B>(608) 824-2800</B>


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</TR>
<TR>
    <TD nowrap>(Former name or former address if changed since last report.)</TD>
</TR>
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<P align="left" style="font-size: 10pt">Check the appropriate box below if the Form 8-K filing is intended to simultaneously satisfy the filing obligation of the registrant
under any of the following provisions:

<P align="left" style="font-size: 10pt">
<FONT face="Wingdings">&#111;</FONT> Written communications pursuant to Rule 425 under the Securities Act (17 CFR 230.425)<BR><BR>
<FONT face="Wingdings">&#111;</FONT> Soliciting material pursuant to Rule 14a-12 under the Exchange Act (17 CFR 240.14a-12)<BR><BR>
<FONT face="Wingdings">&#111;</FONT> Pre-commencement communications pursuant to Rule 14d-2(b) under the Exchange Act (17 CFR 240.14d-2(b))<BR><BR>
<FONT face="Wingdings">&#111;</FONT> Pre-commencement communications pursuant to Rule 13e-4(c) under the Exchange Act (17 CFR 240.13e-4(c))<BR>


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<P align="center" style="font-size: 10pt; display: none">1
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<P align="left" style="font-size: 10pt"><B>Item&nbsp;5.02. Departure of Directors or Certain Officers; Election of Directors; Appointment of Certain Officers;
Compensatory Arrangements of Certain Officers.</B>


<P align="left" style="font-size: 10pt">Effective April&nbsp;15, 2009, the Board of Directors (the &#147;Board&#148;) of TomoTherapy Incorporated (the &#147;Company&#148;)&nbsp;expanded the
size of the Board from nine to ten members and appointed H. Jonathan McCloskey, age 40, as a director of the Company.
Mr.&nbsp;McCloskey was appointed to the Board pursuant to that certain agreement, dated April&nbsp;7, 2009 (the &#147;Agreement&#148;),
among Avalon Capital Group, Inc., Avalon Portfolio, LLC, Avalon Technology, LLC (collectively, the &#147;Avalon Parties&#148;)
and the Company settling the Avalon Parties&#146; proxy contest regarding the election of directors to the Board at the
Company&#146;s 2009 annual meeting of shareholders scheduled for May&nbsp;1, 2009 (the &#147;2009 Annual Meeting&#148;). Mr.&nbsp;McCloskey
will stand for reelection at the 2009 Annual Meeting along with the other nine current members of the Board.


<P align="left" style="font-size: 10pt">Mr.&nbsp;McCloskey is Portfolio Manager of Avalon Capital Group, Inc., a private investment company.&nbsp; He has managed the
interests of Avalon Capital Group, Inc. in its private and public portfolio companies since December&nbsp;2003.&nbsp; Prior to
joining Avalon, Mr.&nbsp;McCloskey was a Vice President of Investment Banking for First Albany Corporation in New York.&nbsp; Mr.
McCloskey is a Director of the San Diego County Board of Retirement, which oversees the investments of the county&#146;s
retirement fund.&nbsp; Mr.&nbsp;McCloskey received a Bachelors of Science degree in Economics from Pennsylvania State University
and a Masters Degree in Business Administration from Yale University.


<P align="left" style="font-size: 10pt">Also effective April&nbsp;15, 2009, the Board appointed Mr.&nbsp;McCloskey to the Company&#146;s Nominating and Governance Committee.


<P align="left" style="font-size: 10pt">In connection with Mr.&nbsp;McCloskey&#146;s appointment to the Board, he has executed the standard confidentiality agreement and
indemnification agreement for directors and will be entitled to receive the customary compensation for non-management
directors as described under &#147;Corporate Governance and Board of Directors Matters&#151;Director Compensation&#148; in the
Company&#146;s definitive proxy statement on Schedule&nbsp;14A, which the Company filed with the Securities and Exchange
Commission (the &#147;SEC&#148;) on March&nbsp;24, 2009.


<P align="left" style="font-size: 10pt">The description of the Agreement contained in Item&nbsp;1.01 of the current report on Form 8-K, which the Company filed with
the SEC on April&nbsp;8, 2009, is incorporated herein by reference.


<P align="left" style="font-size: 10pt"><B>Item&nbsp;9.01. Financial Statements and Exhibits.</B>


<P>
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<TR valign="top" style="font-size: 10pt; color: #000000; background: transparent">
    <TD width="3%" nowrap align="left">(d)</TD>
    <TD width="1%">&nbsp;</TD>
    <TD>Exhibits.</TD>
</TR>

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    <TD nowrap align="left" style="border-bottom: 1px solid #000000">Number</TD>
    <TD>&nbsp;</TD>
    <TD nowrap align="center" style="border-bottom: 1px solid #000000">Description</TD>
</TR>

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<TR valign="bottom">
    <TD valign="top"><DIV style="margin-left:0px; text-indent:-0px"><BR>99.1(1)
</DIV></TD>
    <TD>&nbsp;</TD>
    <TD align="left" valign="top"><BR>Agreement dated April&nbsp;7, 2009, among the Company, Avalon
Capital Group, Inc., Avalon Portfolio, LLC and Avalon Technology,
LLC</TD>
</TR>
<TR valign="bottom">
    <TD valign="top"><DIV style="margin-left:0px; text-indent:-0px"><BR>99.2(1)
</DIV></TD>
    <TD>&nbsp;</TD>
    <TD align="left" valign="top"><BR>Press Release dated April&nbsp;8, 2009, titled &#147;TomoTherapy and
Avalon Announce Settlement: Jonathan McCloskey to Join
TomoTherapy Board of Directors; TomoTherapy to Add Another
Independent Director&#148;</TD>
</TR>
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<TR valign="top" style="font-size: 10pt; color: #000000; background: transparent">
    <TD width="3%" nowrap align="left">(1)</TD>
    <TD width="1%">&nbsp;</TD>
    <TD>Previously filed as an exhibit to the Company&#146;s current report on Form 8-K filed with the SEC on April&nbsp;8, 2009
(File No.&nbsp;001-33452).</TD>
</TR>


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<P align="center" style="font-size: 10pt"><B>SIGNATURES</B>



<P align="left" style="font-size: 10pt; text-indent: 2%">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Pursuant to the requirements of the Securities Exchange Act of 1934, the registrant has duly caused this
report to be signed on its behalf by the undersigned hereunto duly authorized.



<P align="left" style="margin-left:46%; font-size: 10pt"><B>TOMOTHERAPY INCORPORATED</B>


<P align="left" style="font-size: 10pt">Dated: April&nbsp;16, 2009



<P align="left" style="margin-left:46%; font-size: 10pt; margin-top: -11pt">By: <U><B>/</B>s/ Frederick A. Robertson, M.D.&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</U>
<BR>
Frederick A. Robertson, M.D.
<BR>
<I>Chief Executive Officer and President</I>

<P align="center" style="font-size: 10pt">&nbsp;

<P align="center" style="font-size: 10pt; display: none">3
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<P align="center" style="font-size: 10pt">Exhibit&nbsp;Index


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<!-- Begin Table Head -->
<TR valign="bottom">
    <TD width="16%">&nbsp;</TD>
    <TD width="5%">&nbsp;</TD>
    <TD width="79%">&nbsp;</TD>
</TR>
<TR style="font-size: 10pt" valign="bottom">
    <TD nowrap align="left" style="border-bottom: 1px solid #000000">Exhibit No.</TD>
    <TD>&nbsp;</TD>
    <TD nowrap align="center" style="border-bottom: 1px solid #000000">Description</TD>
</TR>

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<TR valign="bottom">
    <TD valign="top"><DIV style="margin-left:0px; text-indent:-0px"><BR>99.1(1)
</DIV></TD>
    <TD>&nbsp;</TD>
    <TD align="left" valign="top"><BR>Agreement dated April&nbsp;7, 2009, among the Company, Avalon
Capital Group, Inc., Avalon Portfolio, LLC and Avalon Technology,
LLC</TD>
</TR>
<TR valign="bottom">
    <TD valign="top"><DIV style="margin-left:0px; text-indent:-0px"><BR>99.2(1)
</DIV></TD>
    <TD>&nbsp;</TD>
    <TD align="left" valign="top"><BR>Press Release dated April&nbsp;8, 2009, titled &#147;TomoTherapy and
Avalon Announce Settlement: Jonathan McCloskey to Join
TomoTherapy Board of Directors; TomoTherapy to Add Another
Independent Director&#148;</TD>
</TR>
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<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="3%" nowrap align="left">(1)</TD>
    <TD width="1%">&nbsp;</TD>
    <TD>Previously filed as an exhibit to the Company&#146;s current report on Form 8-K filed with the SEC on April&nbsp;8, 2009
(File No.&nbsp;001-33452).</TD>
</TR>

</TABLE>


<P align="center" style="font-size: 10pt">&nbsp;

<P align="center" style="font-size: 10pt; display: none">4




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Form 8-K
UNITED STATES
SECURITIES AND EXCHANGE COMMISSION
Washington, D.C. 20549
FORM 8-K
CURRENT REPORT
Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934
Date of Report (Date of earliest event reported): April 15, 2009
TOMOTHERAPY INCORPORATED
(Exact name of registrant as specified in its charter)
Wisconsin
001-33452
39-1914727
(State or other Jurisdiction of Incorporation)
(Commission File Number)
(IRS Employer Identification No.)
1240 Deming Way
Madison, Wisconsin
53717
(Address of Principal Executive Offices)
(Zip Code)
Registrant's telephone number, including area code:
(608) 824-2800
(Former name or former address if changed since last report.)
Check the appropriate box below if the Form 8-K filing is intended to simultaneously satisfy the filing obligation of the registrant
under any of the following provisions:
o
Written communications pursuant to Rule 425 under the Securities Act (17 CFR 230.425)
o
Soliciting material pursuant to Rule 14a-12 under the Exchange Act (17 CFR 240.14a-12)
o
Pre-commencement communications pursuant to Rule 14d-2(b) under the Exchange Act (17 CFR 240.14d-2(b))
o
Pre-commencement communications pursuant to Rule 13e-4(c) under the Exchange Act (17 CFR 240.13e-4(c))
Item 5.02. Departure of Directors or Certain Officers; Election of Directors; Appointment of Certain Officers;
Compensatory Arrangements of Certain Officers.
Effective April 15, 2009, the Board of Directors (the "Board") of TomoTherapy Incorporated (the "Company") expanded the
size of the Board from nine to ten members and appointed H. Jonathan McCloskey, age 40, as a director of the Company.
Mr. McCloskey was appointed to the Board pursuant to that certain agreement, dated April 7, 2009 (the "Agreement"),
among Avalon Capital Group, Inc., Avalon Portfolio, LLC, Avalon Technology, LLC (collectively, the "Avalon Parties")
and the Company settling the Avalon Parties' proxy contest regarding the election of directors to the Board at the
Company's 2009 annual meeting of shareholders scheduled for May 1, 2009 (the "2009 Annual Meeting"). Mr. McCloskey
will stand for reelection at the 2009 Annual Meeting along with the other nine current members of the Board.
Mr. McCloskey is Portfolio Manager of Avalon Capital Group, Inc., a private investment company.  He has managed the
interests of Avalon Capital Group, Inc. in its private and public portfolio companies since December 2003.  Prior to
joining Avalon, Mr. McCloskey was a Vice President of Investment Banking for First Albany Corporation in New York.  Mr.
McCloskey is a Director of the San Diego County Board of Retirement, which oversees the investments of the county's
retirement fund.  Mr. McCloskey received a Bachelors of Science degree in Economics from Pennsylvania State University
and a Masters Degree in Business Administration from Yale University.
Also effective April 15, 2009, the Board appointed Mr. McCloskey to the Company's Nominating and Governance Committee.
In connection with Mr. McCloskey's appointment to the Board, he has executed the standard confidentiality agreement and
indemnification agreement for directors and will be entitled to receive the customary compensation for non-management
directors as described under "Corporate Governance and Board of Directors Matters—Director Compensation" in the
Company's definitive proxy statement on Schedule 14A, which the Company filed with the Securities and Exchange
Commission (the "SEC") on March 24, 2009.
The description of the Agreement contained in Item 1.01 of the current report on Form 8-K, which the Company filed with
the SEC on April 8, 2009, is incorporated herein by reference.
Item 9.01. Financial Statements and Exhibits.
(d)
Exhibits.
Number
Description
99.1(1)
Agreement dated April 7, 2009, among the Company, Avalon
Capital Group, Inc., Avalon Portfolio, LLC and Avalon Technology,
LLC
99.2(1)
Press Release dated April 8, 2009, titled "TomoTherapy and
Avalon Announce Settlement: Jonathan McCloskey to Join
TomoTherapy Board of Directors; TomoTherapy to Add Another
Independent Director"
(1)
Previously filed as an exhibit to the Company's current report on Form 8-K filed with the SEC on April 8, 2009
(File No. 001-33452).
SIGNATURES
Pursuant to the requirements of the Securities Exchange Act of 1934, the registrant has duly caused this
report to be signed on its behalf by the undersigned hereunto duly authorized.
TOMOTHERAPY INCORPORATED
Dated: April 16, 2009
By:
/
s/ Frederick A. Robertson, M.D.
Frederick A. Robertson, M.D.
Chief Executive Officer and President
Exhibit Index
Exhibit No.
Description
99.1(1)
Agreement dated April 7, 2009, among the Company, Avalon
Capital Group, Inc., Avalon Portfolio, LLC and Avalon Technology,
LLC
99.2(1)
Press Release dated April 8, 2009, titled "TomoTherapy and
Avalon Announce Settlement: Jonathan McCloskey to Join
TomoTherapy Board of Directors; TomoTherapy to Add Another
Independent Director"
(1)
Previously filed as an exhibit to the Company's current report on Form 8-K filed with the SEC on April 8, 2009
(File No. 001-33452).