STOP Act of 2009

Security through Termination Of Proliferation Act of 2009 or the STOP Act of 2009 - States that specified U.S. sanctions with respect to Iran, North Korea, or Syria shall remain in effect until the President certifies to the appropriate congressional committees that such country has verifiably dismantled its weapons of mass destruction programs.

Amends the Iran, North Korea, and Syria Nonproliferation Act to include within the scope of such Act (including identification/reporting and sanction provisions) persons involved in the transshipment (as defined by this Act) of certain goods, services, or technology.

Establishes restrictions on nuclear cooperation with a country that is assisting the nuclear program of, or transferring advanced conventional weapons or missiles to, Iran, North Korea, or Syria.

Provides for exclusion from the United States (with a discretionary national security waiver by the President) of an alien who is a senior government official of a foreign government or a corporate principal or significant shareholder of a foreign person identified as involved in proliferation activities respecting Iran, North Korea, or Syria.

Amends the Internal Revenue Code to: (1) deny a foreign tax credit to a taxpayer engaged in business activity with Iran that is prohibited by U.S. law; and (2) set forth income tax provisions respecting a foreign corporation engaged in business activity with Iran that is prohibited by U.S. law.

Establishes the Compensation for Former United States Hostages in Iran Fund.