Characterization and non-invasive measurement of host-pathogen interactions in living cells, animal models and humans at the cellular and molecular levels is now possible using remote imaging detectors. Positron emission tomography scanners, highly sensitive cooled charge-coupled device cameras for bioluminescence and fluorescence imaging as well as high-magnetic-field magnetic resonance imaging scanners can be used to study such diverse processes as pathogen tropism, pathogen life cycle, signal transduction, host response, cell trafficking and gene transfer. In many cases, images from more than one modality can be fused, allowing structure-function and multifunction relationships to be studied on a tissue-restricted or regional basis. These new instruments, when used in conjunction with targeted contrast agents, reporter substrates and radiopharmaceuticals, enable "molecular imaging" with enormous potential for elucidating host-pathogen interactions in intact animal models.