Combined X-Ray CT/Neutron Material Identification System A system and methods for identifying contents of an enclosure such as an air cargo container. A three-dimensional image indicative of at least one of the CT number and the density of contents of the enclosure is obtained using penetrating radiation such as x-rays. If one or more suspect regions are identified among contents of the enclosure, a collimated neutron beam is activated to traverse each suspect region and fluorescent emission from the suspect region is detected, allowing material within the suspect region to be characterized based at least on the detected fluorescent emission. Additionally, the collimated neutron beam may be employed for neutron imaging of the contents of the enclosure.