Purpose: This study was performed to analyze human maxillary and mandibular trabecular bone using the data acquired from micro-computed tomography (micro-CT), and to characterize the site-specific microstructures of trabeculae. Materials and Methods: Sixty-nine cylindrical bone specimens were prepared from the mandible and maxilla. They were divided into 5 groups by region: the anterior maxilla, posterior maxilla, anterior mandible, posterior mandible, and mandibular condyle. After the specimens were scanned using a micro-CT system, three-dimensional microstructural parameters such as the percent bone volume, bone specific surface, trabecular thickness, trabecular separation, trabecular number, structure model index, and degrees of anisotropy were analyzed. Results: Among the regions other than the condylar area, the anterior mandibular region showed the highest trabecular thickness and the lowest value for the bone specific surface. On the other hand, the posterior maxilla region showed the lowest trabecular thickness and the highest value for the bone specific surface. The degree of anisotropy was lowest at the anterior mandible. The condyle showed thinner trabeculae with a more anisotropic arrangement than the other mandibular regions. Conclusion: There were microstructural differences between the regions of the maxilla and mandible. These results suggested that different mechanisms of external force might exist at each site.