Exhibit 16.1 November 3, 2005 Securities and Exchange Commission 100 F Street, N.E. Washington, D.C. 20549 We have been furnished with a copy of the response to Item 4.01 of Form 8-K for the event that occurred on October 31, 2005, to be filed by VA Software Corporation. We agree with the statements made in response to that Item insofar as they relate to our Firm. Very truly yours, /s/ BDO Seidman, LLP BDO Seidman, LLP San Jose, California