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) collect data on health care treatments; (4) establish a standing methodology committee for developing the science of comparative effectiveness research; and (5) 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 transferring amounts from the General Fund and the Medicare Federal Hospital Insurance and Federal Supplementary Medical Insurance Trust Funds and by 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 FY2018.

Requires the Comptroller General to report to Congress on the process for making national coverage determinations under the Medicare program.