Patent Reform Act of 2009 - Amends federal patent law to rewrite provisions concerning the conditions for patentability.

Defines "effective filing date of a claimed invention" as the filing date of the patent or the application for patent containing the claim to the invention (thus establishing a first-to-file system).

Revises various other rights and requirements related to patents, including regarding: (1) damages; (2) post-grant procedures; (3) citation of prior art; (4) inter partes reexaminations; (5) submissions by third parties; (6) venue; (7) the regulatory authority of the Patent and Trademark Office; and (8) inequitable conduct.

Replaces the Board of Patent Appeals and Interferences with the Patent Trial and Appeal Board.

Shields a financial institution that infringes by using a check collection system from the infringement remedies of civil actions, injunctions, damages, and attorney's fees, but does not (in specified circumstances) limit the enforcement rights of the patent's original owner. Applies the amendment made by this paragraph to any civil action for infringement pending or filed on or after the date of enactment of this Act.

Establishes a revolving fund to be known as the United States Patent and Trademark Office Public Enterprise Fund. Deposits into the Fund fees received under specified provisions and makes Fund amounts available for all expenses of the U.S. Patent and Trademark Office (USPTO).