Rail and Public Transportation Security Act of 2004

Rail and Public Transportation Security Act of 2004 - Directs the Under Secretary of Homeland Security for Border and Transportation Security to complete a vulnerability assessment of freight and passenger rail transportation for identification of: (1) critical assets and infrastructures and threats to them; (2) vulnerabilities specific to the transportation of hazardous materials via railroad; and (3) security weaknesses in passenger and cargo security, transportation infrastructure, protection systems, procedural policies, communications systems, employee training, emergency response planning, and any other area identified by the assessment. Requires the Under Secretary based on the assessment to develop specific prioritized recommendations for improving rail security.

Directs the Secretary of Transportation to review existing Department of Transportation (DOT) rail regulations to identify areas for revision to improve rail security.

Directs the Comptroller General to study and report to specified congressional committees on the rail passenger transportation security programs in Japan, the European Union (EU), and other foreign countries in order to identify effective rail transportation security measures.

Directs the Under Secretary to: (1) analyze the cost and feasibility of requiring security screening for passengers, baggage, and mail on passenger trains; and (2) conduct a pilot program of random security screening of passengers and baggage at a specified number of passenger rail stations served by Amtrak.

Authorizes the Secretary to make grants to Amtrak for fire and life-safety improvements and infrastructure upgrades to tunnels on the Northeast Corridor.

Directs the Secretary of Homeland Security to ensure that DOT receives timely notification, through the Information Sharing and Analysis Center for Public Transportation, of all credible terrorist threats against public transportation assets.

Directs the Secretary of Homeland Security to award research, development, and demonstration grants to public and private entities to reduce and deter terrorist threats against public transportation systems.

Amends Federal transportation law to direct Amtrak to submit to the National Transportation Safety Board a plan to address the needs of families of passengers involved in rail passenger accidents.

Authorizes the Under Secretary to make grants for certain system-wide Amtrak security upgrades and freight and hazardous materials transportation and passenger rail security upgrades.

Directs the Federal Railroad Administration to set forth certain standards for welded rail and tank car safety improvements.

Requires the Under Secretary to report to specified congressional committees: (1) an assessment of the current system for preclearance and screening of rail and airline passengers and baggage, as well as freight railroad traffic, between the United States and Canada; and (2) information on progress toward finalizing a protocol with Canada on preclearance of rail passengers between the two countries.

Authorizes the Under Secretary to make operating grants and capital grants for mass transportation system security improvements.