Comparative Effectiveness Research Act of 2009 - Amends title XI (General Provisions, Peer Review, and Administrative Simplification) of the Social Security Act 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.
Establishes the Health Care Comparative Effectiveness Research Institute as a nonprofit, nongovernmental corporation to conduct research on the effectiveness of health care treatments, including pharmaceuticals, medical devices and procedures, and other therapies. Requires the Institute to: (1) identify national priorities for comparative clinical effectiveness research; (2) establish and update a research project agenda and provide for peer review of 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 Comparative Effectiveness Research Trust Fund. Provides revenues for the Trust Fund by: (1) transferring amounts from certain appropriations for comparative effectiveness research, from the General Fund, and from the Medicare Federal Hospital Insurance and Federal Supplementary Medical Insurance Trust Funds; and (2) imposing a fee on certain accident or health insurance policies and self-insured health plans. Requires the Comptroller General to review financial audits of the Institute and assess the adequacy and use of funding. Terminates all funding for the Trust Fund after FY2020.