Cargo containers represent the largest area of concern in terms of Custom and Border Protection, security and vulnerability. With an estimated global inventory of over 12 million, the securing, tracking, and inspection of all shipping containers is a difficult task. A large container ship has the capacity to carry in excess of 3,000 containers, making inspection impossible without disrupting shipment.

Terrorists can, and eventually may, exploit the shipping industries deficiencies in cargo security. Potential threats include the smuggling of weapons of mass destruction (WMD), a radiological "dirty" bomb, a conventional explosive device, and transportation of terrorist operatives, as well.

Studies have claimed a Hiroshima sized nuclear detonation at a major seaport would kill fifty thousand to one million people. The container shipping system is an attractive outlet for terrorist activities. X-ray security screening systems for trucks and freight containers may be used to prevent contraband and detect illegal trafficking of prohibited items.