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

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

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

<P style="font-size: 10pt" align="center"><B>Date of Report (Date of earliest
event reported): December 22, 2008</B>



<P style="font-size: 24pt" align="center"><B>TOMOTHERAPY
INCORPORATED<BR>
</B><FONT style="font-size: 10pt">(Exact name of registrant as
specified in its charter) </FONT>
<TABLE style="font-size: 10pt; text-align: center" cellspacing="0"
cellpadding="0" width="100%" border="0">

 <TR>
  <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>
 </TR>
 <TR valign="bottom">
  <TD style="border-bottom: #000000 1px solid"><B>Wisconsin</B></TD>
  <TD>&nbsp;</TD>
  <TD style="border-bottom: #000000 1px solid"><B>001-33452</B></TD>
  <TD>&nbsp;</TD>
  <TD style="border-bottom: #000000 1px solid"><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>

</TABLE>
<TABLE style="font-size: 10pt; text-align: center" cellspacing="0"
cellpadding="0" width="100%" border="0">

 <TR>
  <TD width="49%">&nbsp;</TD>
  <TD width="1%">&nbsp;</TD>
  <TD width="49%">&nbsp;</TD>
 </TR>
 <TR valign="bottom">
  <TD style="border-bottom: #000000 1px solid"><B>1240 Deming Way<BR>
Madison,
Wisconsin<BR>
</B></TD>
  <TD>&nbsp;</TD>
  <TD style="border-bottom: #000000 1px solid"><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 style="font-size: 10pt" align="center">Registrant&#8217;s telephone number,
including area code: <B>(608) 824-2800</B>
<TABLE style="font-size: 10pt; text-align: center" cellspacing="0"
cellpadding="0" width="30%" border="0">

 <TR>
  <TD width="100%">&nbsp;</TD>
 </TR>
 <TR>
  <TD style="border-bottom: #000000 1px solid" nowrap><B>&nbsp;</B></TD>
 </TR>
 <TR>
  <TD nowrap>(Former name or former address if changed since last report.)</TD>
 </TR>

</TABLE>


<P style="font-size: 10pt" align="left">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 style="font-size: 10pt" align="left"><FONT face="Wingdings">o</FONT> Written
communications pursuant to Rule 425 under the Securities Act (17 CFR
230.425)<BR>
<BR>
<FONT face="Wingdings">o</FONT> Soliciting material pursuant
to Rule 14a-12 under the Exchange Act (17 CFR 240.14a-12)<BR>
<BR>
<FONT
face="Wingdings">o</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">o</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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</DIV>

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

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

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style="margin-left: 0.25in; width: 7.2in; font-family: 'Times New Roman',Times,serif">

<P style="font-size: 10pt" align="left"><B>Item&nbsp;1.01. Entry into a
Material Definitive Agreement.</B>

<P style="font-size: 10pt" align="left">Long Term Purchase Agreement with e2v
Inc. and e2v Technologies (UK)&nbsp;Limited

<P style="font-size: 10pt; text-indent: 4%" align="left">On December&nbsp;22,
2008, TomoTherapy Incorporated (the &#8220;Company&#8221;)&nbsp;entered into a
Long Term Purchase Agreement (the &#8220;Supply Agreement&#8221;) with an
effective date of December&nbsp;22, 2008, with e2v Inc., of Elmsford, New York,
and e2v Technologies (UK)&nbsp;Limited (&#8220;e2v Ltd.&#8221;) of Chelmsford,
United Kingdom, for the purchase and sale of solid state modulators, modulator
accessories and magnetron accessories (the &#8220;Products&#8221;). The parties
were previously doing business for the purchase and sale of the Products
strictly through purchase orders.

<P style="font-size: 10pt; text-indent: 4%" align="left">The Products condition
and control the timing and delivery of the radio frequency energy generated by
the magnetron to the linear accelerator. As such, the Products are key
components in the Company&#8217;s Hi Art system. &nbsp;

<P style="font-size: 10pt; text-indent: 4%" align="left">Pursuant to the Supply
Agreement, the Company committed to purchasing specific quantities of the
Products during the initial term of the agreement, within a specified
percentage tolerance margin, unless otherwise agreed upon by the Parties.
Additionally, to the extent necessary to fulfill the required quantities, the
Company committed to purchase all of its manufacturing production requirements
of the Products from e2v Inc. as its sole source for the Products.

<P style="font-size: 10pt; text-indent: 4%" align="left">The parties agreed to
review annually the quantities purchased and forecast and to make adjustments
to the minimum quantities without invoking any default for failure to meet
minimum quantities or lower quantity break pricing bill back for the period, as
long as e2v Inc. remains the sole source for the Products.

<P style="font-size: 10pt; text-indent: 4%" align="left">During the third year
of the agreement, the parties have agreed to review the quantities purchased
and the 12-month forecast to determine within a specified percentage margin
whether the required quantity for each Product is anticipated to be purchased.
If the parties agree that a lesser quantity of any Product will be purchased
during the initial term, then e2v Inc. and e2v Ltd. may adjust the pricing
accordingly. If the price is increased and the Company meets the required
quantity, then e2v Inc. and/or e2v Ltd. is required to credit the Company the
difference for the increased prices. In the event quantities are exceeded, e2v
Inc. agreed to make an effort to extend better pricing to the Company and
extend volume discounts or other cost savings due to the increased quantities.

<P style="font-size: 10pt; text-indent: 4%" align="left">e2v Inc. can terminate
the agreement if the Company does not meet its required quantities, subject to
the tolerance margin, and e2v is not the sole source of supply, or if e2v Inc.
reasonably anticipates the failure will occur and has consulted with the
Company. In such case, e2v Inc. may invoice the Company for the outstanding
balance based on the pricing for the lower quantity purchased.

<P style="font-size: 10pt; text-indent: 4%" align="left">Either party may
terminate the agreement or any purchase order by giving written notice in the
event that: (1)&nbsp;the other party has breached the agreement and been unable
to cure the breach within 90&nbsp;days from receipt of written notice, or
(2)&nbsp;the other party becomes insolvent or undergoes liquidation.

<P style="font-size: 10pt; text-indent: 4%" align="left">The Supply Agreement,
as redacted in accordance with a request for confidential treatment, is
attached hereto as Exhibit&nbsp;10.1 and incorporated herein by reference.

<P style="font-size: 10pt" align="left">Amendment to License Agreement with
Wisconsin Alumni Research Foundation

<P style="font-size: 10pt; text-indent: 4%" align="left">On December&nbsp;23,
2008, TomoTherapy Incorporated (the &#8220;Company&#8221;)&nbsp;entered into an
Amendment (&#8220;Amendment&#8221;) to the License Agreement (&#8220;License
Agreement&#8221;), with an effective date of December&nbsp;16, 2008, with
Wisconsin Alumni Research Foundation (&#8220;WARF&#8221;). The original License
Agreement between the Company and WARF dated February&nbsp;22, 1999 was filed
with the Securities and Exchange Commission (the &#8220;SEC&#8221;) on
April&nbsp;19, 2007 as Exhibit&nbsp;10.4 to the Company&#8217;s S-1
Registration Statement. An Amendment to the License Agreement dated
April&nbsp;16, 2007 was filed with the SEC on September 21, 2007 as Exhibit&nbsp;10.31 to the
Company&#8217;s S-1 Registration Statement. This Amendment serves as a further
Amendment to the License Agreement and is effective as of December&nbsp;16,
2008.


<P style="font-size: 10pt; text-indent: 4%" align="center">&nbsp;

<P style="font-size: 10pt" align="center">&nbsp;
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<P style="font-size: 10pt; text-indent: 4%" align="left">The License Agreement
was amended to, among other things: (1)&nbsp;grant to the Company a first right
of refusal to add fields not included in its licensed field; (2)&nbsp;revise
the royalty payment schedule, whereby the Company pays to WARF a percentage of
the selling price of each unit, option and upgrade starting from the date of
the Amendment; (3)&nbsp;update the schedule of licensed patents to list
additional patents; and (4)&nbsp;amend the description of the licensed field to
explicitly exclude medical applications using ions.

<P style="font-size: 10pt; text-indent: 4%" align="left">The Amendment, as
redacted in accordance with a request for confidential treatment, is attached
hereto as Exhibit 10.2 and incorporated herein by reference.

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

<P style="font-size: 10pt; text-indent: 8%" align="left">(d)&nbsp;Exhibits.
<DIV align="center">
<TABLE style="font-size: 10pt" cellspacing="0" cellpadding="0" width="100%"
border="0">
<!-- Begin Table Head -->

 <TR valign="bottom">
  <TD width="8%">&nbsp;</TD>
  <TD width="5%">&nbsp;</TD>
  <TD width="87%">&nbsp;</TD>
 </TR>
 <TR style="font-size: 10pt" valign="bottom">
  <TD style="border-bottom: #000000 1px solid" nowrap align="center"><B>Number</B></TD>
  <TD>&nbsp;</TD>
  <TD style="border-bottom: #000000 1px solid" nowrap align="center"><B>Description</B></TD>
 </TR>
<!-- End Table Head -->
<!-- Begin Table Body -->
 <TR valign="bottom">
  <TD valign="top" align="center">
<DIV style="margin-left: 0px; text-indent: 0px">10.1* </DIV>
</TD>
  <TD>&nbsp;</TD>
  <TD valign="top" align="left">Long Term Purchase Agreement with e2v Inc. and
e2v Technologies (UK) Limited executed December&nbsp;22, 2008</TD>
 </TR>
 <TR valign="bottom">
  <TD valign="top" align="center">
<DIV style="margin-left: 0px; text-indent: 0px">10.2* </DIV>
</TD>
  <TD>&nbsp;</TD>
  <TD valign="top" align="left">Amendment to License Agreement with Wisconsin
Alumni Research Foundation executed December&nbsp;23, 2008</TD>
 </TR>
<!-- End Table Body -->

</TABLE>
</DIV>

<P style="font-size: 10pt" align="left">*&nbsp;Confidential treatment has
been requested for portions of this exhibit. These portions have been omitted
from the Form 8-K and submitted separately to the Securities and Exchange
Commission.

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

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

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

<P style="font-size: 10pt; text-indent: 4%" align="left">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.

<DIV align="center">
<TABLE style="font-size: 10pt" cellspacing="0" cellpadding="0" width="100%" border="0">
<!-- Begin Table Head -->
 <TR valign="bottom">
  <TD width="55%">&nbsp;</TD>
  <TD width="5%">&nbsp;</TD>
  <TD width="40%">&nbsp;</TD>
 </TR>
 <TR valign="bottom">
  <TD>&nbsp;</TD>
  <TD valign="top" colspan="2" align="center"><B>TOMOTHERAPY INCORPORATED</B></TD>
 </TR>
 <TR valign="bottom">
  <TD>&nbsp;</TD>
 </TR>

 <TR valign="bottom">
  <TD>Dated: December&nbsp;30, 2008</TD>
  <TD>By:</TD>
  <TD valign="top" align="center" style="border-bottom: #000000 1px solid"><I>/s/ Stephen C. Hathaway</I></TD>
 </TR>

 <TR valign="bottom">
  <TD>&nbsp;</TD>
  <TD>&nbsp;</TD>
  <TD valign="top" align="center">Stephen C. Hathaway<BR>
Chief Financial Officer
</TD>
 </TR>
<!-- End Table Body -->
</TABLE>
</DIV>






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

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

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<DIV style="margin-left: 0.25in; width: 7.2in; font-family: 'Times New Roman',Times,serif">



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

<DIV align="center">
<TABLE style="font-size: 10pt" cellspacing="0" cellpadding="0" width="100%" border="0">
<!-- Begin Table Head -->
 <TR valign="bottom">
  <TD width="10%">&nbsp;</TD>
  <TD width="5%">&nbsp;</TD>
  <TD width="85%">&nbsp;</TD>
 </TR>
 <TR style="font-size: 10pt" valign="bottom">
  <TD style="border-bottom: #000000 1px solid" nowrap align="center"><B>Number</B></TD>
  <TD>&nbsp;</TD>
  <TD style="border-bottom: #000000 1px solid" nowrap align="center"><B>Description</B></TD>
 </TR>
<!-- End Table Head -->
<!-- Begin Table Body -->
 <TR valign="bottom">
  <TD valign="top" align="center">
<DIV style="margin-left: 0px; text-indent: 0px">10.1* </DIV>
</TD>
  <TD>&nbsp;</TD>
  <TD valign="top" align="left">Long Term Purchase Agreement with e2v Inc. and
e2v Technologies (UK) Limited executed December&nbsp;22, 2008</TD>
 </TR>
 <TR valign="bottom">
  <TD valign="top" align="center">
<DIV style="margin-left: 0px; text-indent: 0px">10.2* </DIV>
</TD>
  <TD>&nbsp;</TD>
  <TD valign="top" align="left">Amendment to License Agreement with Wisconsin
Alumni Research Foundation executed December&nbsp;23, 2008</TD>
 </TR>
<!-- End Table Body -->
</TABLE>
</DIV>

<P style="font-size: 10pt" align="left">*&nbsp;Confidential treatment has
been requested for portions of this exhibit. These portions have been omitted
from the Form 8-K and submitted separately to the Securities and Exchange
Commission.

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

<P style="font-size: 10pt" align="center">&nbsp;
</DIV>
</BODY>
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{"company-data": {"conformed-name": "TomoTherapy Inc", "cik": "0001317872", "assigned-sic": "3845", "irs-number": "000000000"}, "filing-values": {"form-type": "8-K", "act": "34", "file-number": "001-33452", "film-number": "081275580"}, "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"}}
Filed by Bowne Pure Compliance
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): December 22, 2008
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 1.01. Entry into a
Material Definitive Agreement.
Long Term Purchase Agreement with e2v
Inc. and e2v Technologies (UK) Limited
On December 22,
2008, TomoTherapy Incorporated (the "Company") entered into a
Long Term Purchase Agreement (the "Supply Agreement") with an
effective date of December 22, 2008, with e2v Inc., of Elmsford, New York,
and e2v Technologies (UK) Limited ("e2v Ltd.") of Chelmsford,
United Kingdom, for the purchase and sale of solid state modulators, modulator
accessories and magnetron accessories (the "Products"). The parties
were previously doing business for the purchase and sale of the Products
strictly through purchase orders.
The Products condition
and control the timing and delivery of the radio frequency energy generated by
the magnetron to the linear accelerator. As such, the Products are key
components in the Company's Hi Art system.
Pursuant to the Supply
Agreement, the Company committed to purchasing specific quantities of the
Products during the initial term of the agreement, within a specified
percentage tolerance margin, unless otherwise agreed upon by the Parties.
Additionally, to the extent necessary to fulfill the required quantities, the
Company committed to purchase all of its manufacturing production requirements
of the Products from e2v Inc. as its sole source for the Products.
The parties agreed to
review annually the quantities purchased and forecast and to make adjustments
to the minimum quantities without invoking any default for failure to meet
minimum quantities or lower quantity break pricing bill back for the period, as
long as e2v Inc. remains the sole source for the Products.
During the third year
of the agreement, the parties have agreed to review the quantities purchased
and the 12-month forecast to determine within a specified percentage margin
whether the required quantity for each Product is anticipated to be purchased.
If the parties agree that a lesser quantity of any Product will be purchased
during the initial term, then e2v Inc. and e2v Ltd. may adjust the pricing
accordingly. If the price is increased and the Company meets the required
quantity, then e2v Inc. and/or e2v Ltd. is required to credit the Company the
difference for the increased prices. In the event quantities are exceeded, e2v
Inc. agreed to make an effort to extend better pricing to the Company and
extend volume discounts or other cost savings due to the increased quantities.
e2v Inc. can terminate
the agreement if the Company does not meet its required quantities, subject to
the tolerance margin, and e2v is not the sole source of supply, or if e2v Inc.
reasonably anticipates the failure will occur and has consulted with the
Company. In such case, e2v Inc. may invoice the Company for the outstanding
balance based on the pricing for the lower quantity purchased.
Either party may
terminate the agreement or any purchase order by giving written notice in the
event that: (1) the other party has breached the agreement and been unable
to cure the breach within 90 days from receipt of written notice, or
(2) the other party becomes insolvent or undergoes liquidation.
The Supply Agreement,
as redacted in accordance with a request for confidential treatment, is
attached hereto as Exhibit 10.1 and incorporated herein by reference.
Amendment to License Agreement with
Wisconsin Alumni Research Foundation
On December 23,
2008, TomoTherapy Incorporated (the "Company") entered into an
Amendment ("Amendment") to the License Agreement ("License
Agreement"), with an effective date of December 16, 2008, with
Wisconsin Alumni Research Foundation ("WARF"). The original License
Agreement between the Company and WARF dated February 22, 1999 was filed
with the Securities and Exchange Commission (the "SEC") on
April 19, 2007 as Exhibit 10.4 to the Company's S-1
Registration Statement. An Amendment to the License Agreement dated
April 16, 2007 was filed with the SEC on September 21, 2007 as Exhibit 10.31 to the
Company's S-1 Registration Statement. This Amendment serves as a further
Amendment to the License Agreement and is effective as of December 16,
2008.
The License Agreement
was amended to, among other things: (1) grant to the Company a first right
of refusal to add fields not included in its licensed field; (2) revise
the royalty payment schedule, whereby the Company pays to WARF a percentage of
the selling price of each unit, option and upgrade starting from the date of
the Amendment; (3) update the schedule of licensed patents to list
additional patents; and (4) amend the description of the licensed field to
explicitly exclude medical applications using ions.
The Amendment, as
redacted in accordance with a request for confidential treatment, is attached
hereto as Exhibit 10.2 and incorporated herein by reference.
Item 9.01. Financial Statements
and Exhibits.
(d) Exhibits.
Number
Description
10.1*
Long Term Purchase Agreement with e2v Inc. and
e2v Technologies (UK) Limited executed December 22, 2008
10.2*
Amendment to License Agreement with Wisconsin
Alumni Research Foundation executed December 23, 2008
* Confidential treatment has
been requested for portions of this exhibit. These portions have been omitted
from the Form 8-K and submitted separately to the Securities and Exchange
Commission.
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: December 30, 2008
By:
/s/ Stephen C. Hathaway
Stephen C. Hathaway
Chief Financial Officer
EXHIBIT INDEX
Number
Description
10.1*
Long Term Purchase Agreement with e2v Inc. and
e2v Technologies (UK) Limited executed December 22, 2008
10.2*
Amendment to License Agreement with Wisconsin
Alumni Research Foundation executed December 23, 2008
* Confidential treatment has
been requested for portions of this exhibit. These portions have been omitted
from the Form 8-K and submitted separately to the Securities and Exchange
Commission.