Patient-Centered Outcomes Research Act of 2009

Patient-Centered Outcomes Research Act of 2009 - Amends title XI (General Provisions, Peer Review, and Administrative Simplification) of the Social Security Act (SSA) to provide for a program of comparative effectiveness research for health care. Defines "comparative effectiveness research" as research evaluating and comparing the implications and outcomes of two or more health care strategies to address a particular medical condition for specific patient populations.

Establishes the Patient-Centered Outcomes Research Institute (PCORTI) as a nonprofit, nongovernmental corporation to conduct Iresearch on the effectiveness of health care treatments, including pharmaceuticals, medical devices and procedures, and other therapies. Requires the PCORTI to: (1) identify national priorities for comparative clinical effectiveness research; (2) establish and update a research project agenda for comparative clinical effectiveness research and provide for peer review of primary research; (3) establish a standing methodology committee for developing the science of comparative effectiveness research; and (4) disseminate research findings.

Amends the Internal Revenue Code to establish in the Treasury the Patient-Centered Outcomes Research Trust Fund. Imposes a fee on certain accident or health insurance policies and self-insured health plans to create revenue for the Fund.

Amends the American Recovery and Reinvestment Act of 2009 to require the Federal Coordinating Council for Comparative Effectiveness Research to support the PCORTI.

Directs the Comptroller General of the United States to report to Congress on the process for making national coverage determinations under SSA title XVIII (Medicare).