Physiological conditions and pathophysiological changes in the lungs may affect many applications in aerosol medicine and pulmonary drug delivery. In the diseased lung, spatial heterogeneity in function and structure may cause substantial changes in aerosol transport and local deposition among different lung regions. Non-uniform aerosol deposition affects airway or tissue pharmacological dosing, which could reduce the therapeutic effectiveness of inhalation therapy. This review article presents examples of pulmonary imaging using PET and PET-CT in lung physiology with an emphasis on their implications for aerosol medicine. Measurements of regional ventilation, perfusion, and ventilation/perfusion ratio, by imaging local kinetics of intravenously injected Nitrogen-13 in saline solution, and of pulmonary inflammation, by assessing the regional uptake of the radiotracer (18)F-FDG, are presented. These examples demonstrate that it is possible to access both preexisting conditions, such as heterogeneity of ventilation, perfusion, and/or inflammatory stimuli, which may affect inhalation therapy, and the functional effects of inhaled medications or inflammatory agents on lung regional function. The imaging techniques described could be efficient tools to evaluate quantitatively and noninvasively these processes in vivo. Furthermore, it can be expected that imaging of respiratory structure and function will yield sensitive biomarkers of disease, which will help and speed drug discovery, and the evaluation of novel inhalation therapies.