The authors performed a longitudinal study of the microstructural changes occurring in the mandibular condyle during osteoporosis using the findings obtained from micro-CT. The subjects used in this study were eight Sprague-Dawley rats. Among them, five were administered the immunosuppressant drug FK506 by injection for five weeks, while the other three were administered saline solution in the same manner. Micro-CT images were taken of the bilateral mandibular condyle, hip, and knee joints in all animals on days 1, 8, 15, 22, 29, and 36 following injection. Six indices of morphometric analysis were compared between the two groups. Significant differences were observed in BV/TV, Tb.Th, Tb.N, and Tb.Sp in the mandibular condyle, while trabecular bone density appeared to decrease in the immunosuppressant group on three-dimensional (3D) imaging. And, in comparison with the mandibular condyle and femur, they were similar. These results suggested that osteoporosis affects not only the femur, but also the mandibular condyle.