The ability to visualize molecular processes and cellular regulators of complex pulmonary diseases such as asthma, chronic obstructive pulmonary disease (COPD), or adult respiratory distress syndrome (ARDS), would aid in the diagnosis, differentiation and therapy assessment. Herein, we report the application of normalized transillumination and fluorescence molecular tomography (FMT), for the noninvasive quantitative imaging of the mouse lung in vivo. We demonstrate the ability to visualize and quantitate pulmonary response in a murine model of lipopolysaccharide (LPS) induced airway inflammation. Twenty-four hours prior to imaging, Balb/c female mice were injected via tail vein with 2nmol of a cathepsin-sensitive activatable fluorescent probe (ex: 750nm; em: 780nm) and 2nmol of accompanying intravascular agent (ex: 674nm; em: 694nm). Six hours later, the mice were anesthetized with isoflurane and administered intranasal lipopolysaccharide in sterile 0.9% saline in 25µl aliquots (one per nostril). Fluorescence molecular imaging revealed the in vivo profile of cysteine protease activation and vascular distribution within the lung typifying the inflammatory response to LPS insult. Results were correlated with standard in vitro laboratory tests (western blot, bronchoalveolar lavage or BAL analysis, immuno-histochemistry) and revealed good correlation with the underlying activity. We have demonstrated the capacity of fluorescence tomography to non-invasively and longitudinally characterize physiological, cellular and sub-cellular processes associated with inflammatory disease burden in the lung. The data presented herein serves to further evince fluorescence molecular imaging as a technology highly appropriate for the biomedical laboratory.