The most substantial difference between the two bills is the approach to the airport screening process. The Senate bill would federalize the airport screening process, while the House bill would give the President the flexibility of adopting either a federal-private sector coordination or federalizing the airport screening process. The private-federal model requires the federal government to provide an average of 10 to 15 percent of security personnel while the private sector provides the remaining 85-90 percent of security personnel. A passenger facility fee of $2.50 charged for each one-way trip would cover the cost of increased security. If the fee imposed on passengers is insufficient to pay for the costs of the increased security, a fee will be imposed on the air carriers for the difference between the security cost and the amount collected from passengers. The legislation also makes flexible funds under the Airport Improvement Program and Passenger Facility Charges if the fee or grant is used to improve security at the airport.

H.R. 3150 would establish a new Transportation Security Administration that would oversee security measures for all modes of transportation. The Transportation Security Administration would be headed by a new Under Secretary of Transportation Security. The Under Secretary of Transportation would oversee an expanded federal air marshal program. The Under Secretary would be required to develop methods to strengthen cockpit doors, provide for the use of video monitors to alert the cockpit crew to activity in the passenger cabin and for other innovative technologies. The bill authorizes $500 million to air carriers to carry out increased aircraft security measures.

The legislation would authorize the Department of Justice (DOJ) to hire, train and supervise federal government employees to screen baggage and passengers at major airports across the country. In addition, the DOJ would be authorized to order law enforcement personnel at each airport security screening location. The legislation requires at least one law enforcement officer at each airport security screening location at the 100 largest airports in the U.S. The Attorney General may require that screening of passengers and baggage at smaller airports be carried out by qualified, trained state or local law enforcement personnel and meet federal standards. The cost of this increased security is estimated at $1.2 billion - $2 billion per year. The heightened security would by covered by a fee of $2.50 for each passenger enplanement. The legislation also makes flexible funds under the Airport Improvement Program and Passenger Facility Charges to "defray additional direct security-related expenses imposed by law or rule after September 11, 2001". The government expects the increased security to take at least six months to put in place.

The DOJ would be authorized to oversee an expanded Federal air marshal program.

The Attorney General would define guidelines for the training and deployment of individuals authorized. The Secretary of Transportation could place federal air marshals on every scheduled passenger flight and would place them on every flight that is believed to present high security risks. The measure also authorizes the FAA to allow pilots to carry guns and would also require airplanes to be fitted with reinforced cockpit doors accessible only to pilots.