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A new generation of imaging devices now make it possible to generate both structural and functional images for the study of lung biology in small animals, including common laboratory mouse and rat models. “Micro” X-ray computed tomography and positron emission tomography scanners, highly sensitive cooled charge coupled device cameras for bioluminescence and fluorescence imaging, high magnetic field magnetic resonance imaging scanners, and recent advances in ultrasound system technology can be used to study such diverse processes as ventilation, perfusion, pulmonary hypertension, lung inflammation, and gene transfer, among others. Images from more than one modality can also be fused, allowing structure-function and function-function relationships to be studied on a regional basis. These new instruments, part of an emerging suite of techniques collectively known as “molecular imaging,” provide an enormous potential for elucidating lung biology in intact animal models and systems.