Characterization and noninvasive measurement of molecular pathways and biochemistry in living cells, animal models, and humans at the cellular and molecular level is now possible using remote imaging detectors. Positron and single photon emission tomography scanners, highly sensitive 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 signal transduction, receptor density and function, host response to pathogens, 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. “Molecular imaging” holds enormous potential for elucidating the molecular mechanisms of pulmonary disease and therapeutic response in intact animal models and humans.