Anti-Terrorism Protection of Mass Transportation and Railroad Carriers Act of 2003 - Amends the Federal criminal code to prohibit specified attacks and acts of violence against mass transportation systems and against railroad carriers, including derailing a train, placing a biological agent or toxin in or near a mass transportation vehicle, setting fire to a terminal, committing an act with intent to cause serious bodily injury to a railroad employee, and conveying false information concerning an attempt to commit such a crime. Lists circumstances resulting in aggravated offenses. Sets penalties for violations.

Authorizes: (1) the interception of wire, oral, or electronic communications in cases involving domestic or international terrorism and involving other specified offenses (such as violence at international airports, an attack on a Federal facility with a firearm, and conspiracy to harm persons or property overseas); and (2) the use of an emergency pen register or trap and trace device in cases involving domestic or international terrorism or conspiratorial activities threatening the national security interest.

Modifies the definition of: (1) "Federal crime of terrorism" to include an offense that appears by its nature or context to be intended to intimidate or coerce a civilian population, influence the policy of a government by intimidation or coercion, or affect the conduct of a government by mass destruction, assassination, or kidnaping; and (2) "international terrorism" to include listed actions that appear "by their nature or context" to be intended to intimidate, influence, or affect governmental conduct.