X0202 4 2007-10-16 0 0001317872 TomoTherapy Inc TTPY 0001397868 Hughes John H 1240 DEMING WAY MADISON WI 53717 0 1 0 0 VP of Business Development Common Stock 2007-10-16 4 S 0 89970 22.25 D 121310 D The reporting person's sale of TomoTherapy common stock reported herein was matchable under Section 16(b) of the Securities Exchange Act of 1934, to the extent of 400 shares, with the reporting person's purchase of 400 shares of TomoTherapy common stock at a price of $19 per share on May 9, 2007. The reporting person has agreed to pay to TomoTherapy, upon settlement of the sale, $888.36, representing the full amount of the profit realized in connection with the short-swing transaction, less transaction costs. /s/ Shawn D. Guse, as attorney in fact 2007-10-18