United Nations Transparency, Accountability, and Reform Act of 2009

United Nations Transparency, Accountability, and Reform Act of 2009 - Sets forth U.S. policy with respect to: (1) shifting the funding mechanism for the regular budget of the United Nations from an assessed to a voluntary basis; (2) reform of U.N. peacekeeping operations; and (3) Security Council expansion.

Withholds nonvoluntary U.S. contributions to the regular budget of the United Nations: (1) unless the Secretary of State certifies to the appropriate congressional committees that 80% of the the total regular budget of the United Nations is apportioned on a voluntary basis; and (2) to a U.N. human rights treaty monitoring body or committee that was established by a convention or a covenant to which the United States is not party.

Establishes the Office of the United States Inspector General for Contributions to the United Nations System.

Prohibits the obligation or expenditure of a U.S. contribution to any U.N. entity unless the entity has provided the Inspector General with a transparency certification and is in compliance with such certification.

Directs the Secretary to audit and report to the appropriate congressional committees respecting duplicative entities and efforts related to Israeli-Palestinian issues. Withholds funds for such entities until any report recommendations are implemented.

Directs the President to use U.S. influence at the United Nations with respect to: (1) publication of all U.N. subsidiary bodies and their functions, budgets, staff, and contributions; (2) employee, agency, and funding financial disclosure; (3) waiver of immunity; (4) adoption of a definition of terrorism and a comprehensive convention on terrorism; (5) anti-Semitism at the United Nations; and (6) Israel's inclusion in the Western European and Others Group.

Directs the President to use U.S. influence at the International Atomic Energy Agency (IAEA) to: (1) establish an Office of Compliance in the Secretariat of the IAEA; and (2) prohibit Iran's access to nuclear material, technology, equipment, or assistance until the IAEA determines that Iran is providing full access to IAEA inspectors and has permanently ceased and dismantled all nuclear-enrichment and reprocessing activities.

Directs the Secretary to report to the appropriate congressional committees regarding U.N. reforms and personnel.

Withholds annual U.S. contributions to the United Nations Relief and Works Agency for Palestine Refugees in the Near East (UNRWA) until certain conditions are certified, and then provides UNRWA with limited contributions.

Withholds U.S. contributions to the United Nations Human Rights Council until the Secretary certifies to Congress that the Council does not include a member state: (1) subject to Security Council sanctions; (2) under a Security Council-mandated investigation for human rights abuses; (3) subject, within the prior five years, to a country-specific resolution passed by the former U.N. Human Rights Commission; (4) which the Secretary has determined is a government that has repeatedly provided support for acts of international terrorism; or (5) which the President has designated as a country of particular concern for religious freedom.