New optical techniques have the potential to fill the gap between radiological and microscopic approaches to assess the lung's internal structure. Since its quantitative assessment requires unbiased sampling and measurement principles, imaging of the whole lung with sufficient resolution for visualizing details is important. To address this request, we applied scanning laser optical tomography (SLOT) for the three dimensional imaging of mouse lung ex vivo. SLOT is a highly efficient flourescence and transmission microscopy technique allowing for 3D imaging of specimen of sizes up to several millimeters. Previously fixed lung lobes and whole lungs were optically cleared and subsequently imaged with SLOT while making use of intrinsic contrast mechanisms like absorption and autofluorescence. Imaging of airways, blood vessels and parenchyma is demonstrated. Volumetric SLOT datasets of the lung's internal structure can be analyzed in any preferred planar orientation. Moreover, the sample preparation preserves microscopic structure of the lung and allows for subsequent correlative histologic studies. In summary, SLOT is a useful technique to visualize and survey the internal structure of mouse lung at different scales and with various contrast mechanisms. Potential applications of SLOT in lung research are e.g. quantitative phenotype analysis of mouse models of human lung disease in combination with stereological methods. © (2013) COPYRIGHT Society of Photo-Optical Instrumentation Engineers (SPIE). Downloading of the abstract is permitted for personal use only.