Biomedical imaging has become an important tool in the study of ''-omics'' fields by allowing the noninvasive visualization of functional and molecular events using in vivo staining and reporter gene approaches. This capacity can go beyond the understanding of the genetic basis and phenotype of such respiratory conditions as acute bronchitis, adult respiratory distress syndrome (ARDS), chronic obstructive pulmonary disease (COPD), and asthma and investigate the development of disease and of therapeutic events longitudinally and in unperturbed environments. Herein, we show how the application of novel quantitative optical imaging methods, using transillumination and fluorescence molecular tomography (FMT), can allow visualization of pulmonary inflammation in small animals in vivo. The results confirm prior observations using a proteasesensitive probe. We discuss how this approach enables in vivo insights at the system level as to the dynamic role of proteases in respiratory pathophysiology and their potential as therapeutic targets. Overall, the proposed imaging method can be used with a significantly wider range of possible targets and applications in lung imaging.Keywords: fluorescence; tomography; proteases; lung; inflammation, in vivo Investigation of the respiratory system at the cellular, biochemical, and molecular level is critical in understanding lung disease and designing effective and novel strategies for prevention and intervention. Our knowledge of the cells and mediators that are involved in lung diseases has increased immensely during the last decade (1-3). This knowledge provides the basis for improving the rational development of therapeutic strategies that may relieve or prevent the development of symptoms.Coupled to the importance of understanding the genetic basis and phenotype of the disease is the ability to visualize the associated molecular processes in vivo. Fluorescence molecular tomography (FMT) is a technology developed to quantitatively image the up-regulation and function of tumoral proteases, cellular receptors, and other proteins (4). Recently this technology has been applied to in vivo imaging of brain, mammary, and lung tumors and for studying tumor angiogenesis and chemotherapeutic effects in entire animals (5, 6). The technique may be ideally also suited for studying lung diseases and responses to environmental stimuli noninvasively and in vivo in small animals, especially if multi-projection approaches are implemented (5). This is in contrast to the mainstay of fluorescence imaging techniques currently available, such as microscopy, which does not penetrate under the tissue surface for more than about 500 mm, or photographic methods that penetrate to only superficial depths (z2-3 mm) and yield single projection qualitative images. The FMT application to lung imaging is foreseen to play a markedly different role than microscopy, since the method achieves macroscopic resolutions similar to the ones of nuclear imaging. The benefits of FMT are associated with its ability for three...