Systems, methods and apparatus for detecting concealed security threats by sampling molecules of substances for assessment wherein these molecules may be contained in the air in or near concealed security threats. Inspection of cargo containers by sampling the air contained therein and then analyzing the sampled air from the container for security threats including chemical, biological, radiological, nuclear, and high-explosive threats without requiring the modification of the existing container, the movement of the container to a particular inspection site, and without opening the container. Nuclear security threats may also be scanned for with close proximity nuclear radiation detection sensors closely coupled to areas at or near the concealed security threats. In addition, detection of other types of contraband, including illegal substances, embargoed materials and human and/or animal stowaways may also be assessed. The concealed security threat detection system generally includes a detection system comprising a detector array, an air-moving device, and one or more air-sampling devices. This system may be mounted upon a vehicle for mobility, run on tracks, cables and pulleys, telescoping and swiveling arms, etc.