Directs the Secretary of Transportation to review existing Department of Transportation (DOT) rail regulations to identify areas in which those regulations need to be revised 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, member nations of the European Union (EU), and other foreign countries in order to identify effective rail transportation security measures in use in those foreign rail transportation systems, including innovative measures and screening procedures determined effective.

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 appropriations for Amtrak for certain fire and life-safety improvements and infrastructure upgrades to tunnels on the Northeast Corridor.

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.

Establishes a research and development (R&D) program to improve freight and intercity passenger rail security.

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 protocal with Canada on preclearance of rail passengers between the two countries.

Requires the Under Secretary, based on the assessment, to develop specific prioritized recommendations for improving rail security, including: (1) improving the security of rail tunnels, rail bridges, rail switching and car storage areas, other rail infrastructure and facilities, information systems, and other areas identified as posing significant rail-related risks to public safety and the movement of interstate commerce; (2) deploying equipment to detect explosives and hazardous chemical, biological, and radioactive substances, and any appropriate countermeasures; (3) training employees in terrorism prevention, passenger evacuation, and response activities; and (4) deploying surveillance equipment. Directs the Under Secretary to report to specified congressional committees on the assessment, prioritized recommendations, and an estimate of the cost to implement such recommendations, with biennial updates.

Authorizes appropriations for FY 2005.

(Sec. 3) Directs the Secretary of Transportation (Secretary) to review existing Department of Transportation (DOT) rail regulations to identify areas in which those regulations need to be revised to improve rail security.

(Sec. 4) Directs the Comptroller General to study and report to specified congressional committees on the rail passenger transportation security programs in Japan, member nations of the European Union (EU), and other foreign countries in order to identify effective rail transportation security measures in use in those foreign rail transportation systems, including innovative measures and screening procedures determined effective, and an assessment of whether it is feasible to implement such security measures in the United States.

(Sec. 5) Directs the Under Secretary to: (1) analyze the cost and feasibility of requiring security screening for passengers, baggage, and cargo on passenger trains; and (2) conduct a pilot program of random security screening of passengers and baggage at five passenger rail stations served by Amtrak. Authorizes appropriations for FY 2005.

(Sec. 6) Declares that certain personnel limitations on the number of employees in the Transportation Security Administration (TSA) of the DOT (before or after its transfer to the Department of Homeland Security) shall not apply.

(Sec. 7) Authorizes appropriations for FY 2005 through 2009 for Amtrak for certain fire and life-safety improvements and infrastructure upgrades to its tunnels on the Northeast Corridor. Prohibits the Secretary from making amounts available to Amtrak until it has submitted, for the Secretary's approval, an engineering and financial plan for such projects, and the Secretary has approved an Amtrak project management plan.

(Sec. 8) Directs the Secretary of Homeland Security to execute a memorandum of agreement governing the roles and responsibilities of the DOT and the Department of Homeland Security in addressing railroad transportation security, including the processes the departments will follow to promote communications, efficiency, and nonduplication of effort.

(Sec. 9) 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. Declares that Amtrak shall not be liable for damages in actions brought in a Federal or State court arising out of the performance of Amtrak in preparing or providing a passenger list, or in providing information concerning a train reservation, unless such liability was caused by Amtrak's conduct. Authorizes appropriations for FY 2005.

(Sec. 10) 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. Authorizes appropriations for FY 2005.

(Sec. 13) Establishes a research and development (R&D) program to improve freight and intercity passenger rail security, including R&D projects to: (1) reduce the vulnerability of passenger trains, stations, and equipment to explosives and hazardous chemical, biological, and radioactive substances; (2) develop improved freight technologies; (3) test wayside detectors that can detect tampering with railroad equipment; and (4) support enhanced security for the transportation of hazardous materials by rail. Authorizes appropriations for FY 2005 and 2006.

(Sec. 14) Directs the Federal Railroad Administration (FRA) to set forth certain standards for welded rail and tank car safety improvements. Directs the FRA to: (1) analyze the impact resistance of the steels in the shells of pressure tank cars constructed before 1989; and (2) report to specified congressional committees recommendations for measures to eliminate or mitigate the risk of catastrophic failure.

(Sec. 15) 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.

(Sec. 16) Directs the Secretary of Homeland Security to study and report to specified congressional committees on the impact of blocked highway-railroad grade crossings on the ability of emergency responders, including ambulances and police, fire, and other emergency vehicles, to perform public safety and security duties in the event of a terrorist attack.

(Sec. 17) Sets forth certain whistleblower protections, including prohibition of discrimination, a dispute resolution procedure, and remedies, for rail employees or other persons acting on behalf of such employees who have provided information to the employer or the Federal Government, or provided testimony before Congress or at a Federal or State proceeding, regarding a perceived threat to security, or who have refused to violate or assist in the violation of any regulation related to rail security.

Rail Security Act of 2004 - (Sec. 2) 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 such assets and infrastructures; (2) vulnerabilities that are 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, including: (1) improving the security of rail tunnels, rail bridges, rail switching and car storage areas, other rail infrastructure and facilities, information systems, and other areas identified as posing significant rail-related risks to public safety and the movement of interstate commerce; (2) deploying equipment to detect explosives and hazardous chemical, biological, and radioactive substances, and any appropriate countermeasures; (3) training employees in terrorism prevention, passenger evacuation, and response activities; and (4) deploying surveillance equipment. Directs the Under Secretary to report to specified congressional committees on the assessment, prioritized recommendations, and an estimate of the cost to implement such recommendations, with biennial updates.

Authorizes appropriations for FY 2005.

(Sec. 3) Directs the Secretary of Transportation (Secretary) to review existing Department of Transportation (DOT) rail regulations to identify areas in which those regulations need to be revised to improve rail security.

(Sec. 4) Directs the Comptroller General to study and report to specified congressional committees on the rail passenger transportation security programs in Japan, member nations of the European Union (EU), and other foreign countries in order to identify effective rail transportation security measures in use in those foreign rail transportation systems, including innovative measures and screening procedures determined effective, and an assessment of whether it is feasible to implement such security measures in the United States.

(Sec. 5) Directs the Under Secretary to: (1) analyze the cost and feasibility of requiring security screening for passengers, baggage, and cargo on passenger trains; and (2) conduct a pilot program of random security screening of passengers and baggage at five passenger rail stations served by Amtrak. Authorizes appropriations for FY 2005.

(Sec. 6) Declares that certain personnel limitations on the number of employees in the Transportation Security Administration (TSA) of the DOT (before or after its transfer to the Department of Homeland Security) shall not apply.

(Sec. 7) Authorizes appropriations for FY 2005 through 2009 for Amtrak for certain fire and life-safety improvements and infrastructure upgrades to its tunnels on the Northeast Corridor. Prohibits the Secretary from making amounts available to Amtrak until it has submitted, for the Secretary's approval, an engineering and financial plan for such projects, and the Secretary has approved an Amtrak project management plan.

(Sec. 8) Directs the Secretary of Homeland Security to execute a memorandum of agreement governing the roles and responsibilities of the DOT and the Department of Homeland Security in addressing railroad transportation security, including the processes the departments will follow to promote communications, efficiency, and nonduplication of effort.

(Sec. 9) 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. Declares that Amtrak shall not be liable for damages in actions brought in a Federal or State court arising out of the performance of Amtrak in preparing or providing a passenger list, or in providing information concerning a train reservation, unless such liability was caused by Amtrak's conduct. Authorizes appropriations for FY 2005.

(Sec. 10) 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. Authorizes appropriations for FY 2005.

(Sec. 13) Establishes a research and development (R&D) program to improve freight and intercity passenger rail security, including R&D projects to: (1) reduce the vulnerability of passenger trains, stations, and equipment to explosives and hazardous chemical, biological, and radioactive substances; (2) develop improved freight technologies; (3) test wayside detectors that can detect tampering with railroad equipment; and (4) support enhanced security for the transportation of hazardous materials by rail. Authorizes appropriations for FY 2005 and 2006.

(Sec. 14) Directs the Federal Railroad Administration (FRA) to set forth certain standards for welded rail and tank car safety improvements. Directs the FRA to: (1) analyze the impact resistance of the steels in the shells of pressure tank cars constructed before 1989; and (2) report to specified congressional committees recommendations for measures to eliminate or mitigate the risk of catastrophic failure.

(Sec. 15) 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.

(Sec. 16) Directs the Secretary of Homeland Security to study and report to specified congressional committees on the impact of blocked highway-railroad grade crossings on the ability of emergency responders, including ambulances and police, fire, and other emergency vehicles, to perform public safety and security duties in the event of a terrorist attack.

(Sec. 17) Sets forth certain whistleblower protections, including prohibition of discrimination, a dispute resolution procedure, and remedies, for rail employees or other persons acting on behalf of such employees who have provided information to the employer or the Federal Government, or provided testimony before Congress or at a Federal or State proceeding, regarding a perceived threat to security, or who have refused to violate or assist in the violation of any regulation related to rail security.