Background: Optical coherence tomography (OCT) is an evolving technology that is capable of delivering real-time, high-resolution images of tissues. The purpose of this study was to evaluate the feasibility of using OCT for detecting airway pathology in a septic animal model. Methods: The tracheas of New Zealand white rabbits were inoculated endobronchially with various concentrations of live Streptococcus pneumoniae bacteria. After the development of pneumonia/sepsis, the animals were killed. OCT tracheal images and corresponding histologic specimens from these experimental animals were compared to control rabbit tracheas for morphologic features and quantitative tracheal mucosal thickness measurements. Results: The results revealed significant airway mucosal thickening in the experimental group that was consistent with tracheal edema. Morphologic changes, including epithelial denuding and mucosal sloughing, were evident in regions of the experimental tracheas. Conclusion: This study suggests that OCT is a potentially valuable imaging modality that is capable of evaluating superficial airway pathology with high-resolution in vivo images. Numerous applications of OCT can be envisioned in the realm of pulmonary medicine and thoracic surgery that may substantially increase the precision and accuracy of current bronchoscopic diagnostic and surgical techniques.