This study investigated the three dimensional (3D) trabecular microstructure of the alveolar and basal bone in the mandible using micro-CT and compared the morphometric values of the different sites. Ten specimens were prepared and scanned using a micro-CT system. Both the alveolar and basal trabecular bone of the premolar region in the mandible were measured for the structural analysis. Cross-sectional 1024·1024 pixel images were created. From the two-dimensional (2D) images produced, 3D structural images were reconstructed. After scanning the specimen, the volumes of interest (VOI) of the alveolar and basal bone regions were selected from the 3D reconstruction images, and the structural parameters such as bone volume fraction, bone surface density, trabecular thickness, trabecular separation, trabecular number and structural model index were analyzed. The trabecular structure showed a marked variation within the sites of the specimen, especially in the basal trabecular bone inferior to the mandibular canal. In both the alveolar and basal bone regions, a mixture of both plate-like and rod-like structures was observed. The alveolar region showed a more compact, plate-type trabecular structure than the basal regions. In parametric comparison with the basal bone, the alveolar bone generally had a higher bone volume fraction, bone trabecular thickness and trabecular number, and lower bone surface density, trabecular separation and structural model index. The alveolar bone consisted of a compact bone structure with a large amount of thick plate-type trabecular bone, which was effectively resistant to the masticatory forces. As the measurements were made closer to the basal bone, a loose structure was observed with lower bone volume and fewer, thin, rod-like trabeculae.