Accurate lung morphometry is fundamental for predicting aerosol dosimetry. Currently, lung morphometry is only available for two to three species of mice (B6C3F1, Balb/c, and AJ). Based upon in situ-prepared silicone rubber mouse lung casts, a complete process, including their micro-CT scanning, segmentation, and automated algorithmic processing enabling the determination of airway geometries, was developed for four strains of mice (Balb/c, AJ, ApoE, and C57BL6). In situ-prepared silicone rubber lung casts were prepared from 20 ApoE and C57BL6 mice. The cured mouse lung casts were manually inspected for casting quality, and selected mouse casts had manual morphometry measurements performed (tracheobronchial generations 1-6) prior to high-resolution micro-CT scanning. Micro-CT scanning of existing in situ lung casts from Balb/c and AJ mice were also performed. Micro-CT images were then segmented to reconstruct a 3D model of the lung casts. A skeleton of each processed lung cast was automatically created by shrinking the 3D model of each airway to its centerline. Algorithms were developed for automatic detection of possible skeleton exceptions, including closed loops, trifurcations, and isolated nodes, to be subsequently manually resolved. Finally, the skeleton was automatically measured extracting major airway morphometry characteristics (airway generation number, length, diameter, bifurcations angles, and angle to gravity). The automated measurement procedure was tested/verified by comparing its measurements of airway length, diameter, and bifurcation angles with previous manual morphometry measurements from the identical Balb/c and AJ mouse lung casts and automated measurements of two Balb/c mouse lung casts. Not surprisingly, tracheobronchial airway diameters for ApoE and C57BL6 mice were similar, but were significantly different from the other mice species/strains examined. It is anticipated that these anatomical differences will result in different aerosol deposition, as predicted by various dosimetry codes (NCRP, ICRP, and Multiple-Path Particle Dosimetry Model).