Railroad Antitrust Enforcement Act of 2006

Railroad Antitrust Enforcement Act of 2006 - Amends the Clayton Act to grant the United States exclusive authority to bring suit for injunctive relief against a common carrier that is not a rail common carrier subject to the jurisdiction the Surface Transportation Board (STB).

Revises the declaration that prohibitions against mergers and acquisitions that tend to create monopolies shall not apply to certain transactions duly consummated pursuant to specified federal authority. Excepts specified rate agreements between two or more rail carriers (collective rate agreements) and certain transactions, including railroad mergers and acquisitions, from specified antitrust exemptions.

Provides that, in any civil action against a rail common carrier, the U.S. district court shall not be required to defer to the primary jurisdiction of the STB.

Empowers the Federal Trade Commission to regulate, and engage in antitrust enforcement regarding, collective rate agreements and certain transactions, including railroad mergers and acquisitions.

Applies to rail common carriers subject to STB jurisdiction requirements governing the amount of recovery or prejudgment interest (treble damages) by injured persons, without regard to whether: (1) such railroads have filed rates; or (2) a complaint has been filed that challenges a rate.

Amends federal transportation law to terminate the exemptions from antitrust laws for collective ratemaking agreements.

Requires the STB, and other reviewing agencies, when reviewing a proposed agreement, to take into account its impact upon shippers, consumers, and affected communities.

Revises STB authority to provide that a rail carrier, corporation, or a person participating in an approved transaction is not exempt from specified antitrust laws.