A safe, reliable and rapid system for the detection of nuclear materials within containers includes the use of pulsed high-intensity gamma rays that can penetrate a container and its contents and can be detected outside the container to provide a display in which high-Z material, including lead, uranium, plutonium and other nuclear substances that absorb gamma rays are detected as black regions on the display. In one embodiment, orthogonal pulsed gamma ray beams illuminate the container from two different directions to provide three-dimensional slices from which the existence and location of nuclear threat materials can be ascertained in as little as four seconds for a 40-foot container.