Anti-Atrocity Alien Deportation Act of 2003

Redefines "genocide" for such purposes to cover an alien who has ordered, incited, assisted, or otherwise participated in conduct outside the United States that would, if committed in the United States or by a U.S. national, be genocide (as defined in title 18, United States Code).

Redefines "severe violations of religious freedom" with respect to the inadmissibility and removability of a foreign government official to cover an alien who, while serving as a foreign government official, was responsible for or directly carried out at any time severe violations of religious freedom (as defined in the International Religious Freedom Act of 1998). Eliminates the bar to the admission of such person's spouse or children.

Prohibits the waiver of inadmissibility and temporary admission of such aliens.

Prohibits an alien who has engaged in Nazi persecution, genocide, acts of torture, extrajudicial killings, or severe violations of religious freedom from establishing good moral character under such Act.

Directs the Attorney General to: (1) establish within the Criminal Division of the Department of Justice an Office of Special Investigations to investigate and denaturalize an alien who has participated in Nazi persecution, genocide, torture, or extrajudicial killing abroad; and (2) consult with the Secretary of Homeland Security regarding actions to prosecute or extradite such aliens.

States that in determining the proper legal action against such an alien, consideration shall be given to the availability of U.S. prosecution or removal to a foreign jurisdiction for prosecution.