Amtrak, FY2004-FY2006 Authorization bill

American Rail Equity Act of 2003 - Amends Federal transportation law to establish a National Passenger Rail Office in the Federal Transit Administration of the Department of Transportation to carry out specified responsibilities for the national passenger railroad system.

Includes within such system: (1) the segment of the Northeast Corridor (NEC) between Boston, Massachusetts, and Washington, D.C.; (2) designated high-speed rail corridors; (3) long-distance routes of more than 750 miles between endpoints currently operated by the National Passenger Rail Corporation (Amtrak); and (4) short-distance corridors or routes operated by Amtrak.

Declares that Amtrak shall not be required to be operated or managed as a for-profit corporation. Limits the responsibility of Amtrak to operations relating to the provision of intercity and commuter rail passenger transportation, the transportation of mail and express, auto-ferry transportation, related marketing, and facilities for the maintenance of necessary rolling stock.

Requires the Office to determine whether each Amtrak route met its 80 percent on-time performance goal during the most recent performance period. Prohibits the Office from discontinuing an Amtrak route unless Amtrak failed to meet its on-time performance goal for such route in three out of the immediately preceeding five years.Declares that Amtrak shall forfeit to the Office the right to provide passenger rail transportation on any route on which Amtrak failed to meet its goal during the most recent performance period. Requires the Office to lease such forfeited right to an appropriate person or entity.

Requires the Office on a quarterly basis to identify advisable rail infrastructure improvement projects, and make grants for such projects.

Provides for high-speed corridor planning and grants to assist States or compacts of States to establish corridors for high-speed rail service.

Establishes a non-profit non-governmental Rail Infrastructure Finance Corporation to provide financial support, through issuance of qualified rail infrastructure bonds, for rail transportation capital projects.

Authorizes the Board of the Finance Corporation to make grants to States, compacts of States, or Amtrak for intercity passenger rail capital projects. Limits the total amount of such grants for the NEC to 25 percent of the total amount available.

Amends the Internal Revenue Code to allow a tax credit to holders of qualified rail infrastructure bonds.

Amends Federal transportation law to authorize each State to prepare a rail plan that: (1) sets forth State policy for all freight and passenger rail transportation, including commuter rail operations; and (2) establishes or designates a State rail transportation authority to prepare and administer the plan, as well as a State rail plan approval authority to approve it, subject to the Secretary's approval.

Authorizes the Secretary to designate high priority freight and passenger rail capital projects included in a State rail plan that focus on key rail congestion points selected on the basis of national benefits to the rail transportation system, and coordinated with the national rail plan.