Purpose: The aim of this study was to observe the bony change in the OVX rat longitudinally and to study the alendronate effect. Materials and Methods: Eighteen Sprague-Dewley rats, eight-week old each, were randomly assigned into three groups: one of those sham-operated (N=4), the other two were OVX: saline-treated (N=7) and alendronate-treated group (N=7). The saline-treated group was administered with saline solution (0.1mL/100g) daily, while the alendronate-treated group was given alendronate (1mg/kg, Sigma-Aldrich Corp. Korea) daily. Micro-CT scannings of the lumbar were consecutively done at baseline, at 3-week intervals during 9 weeks. Two and three dimensional bony analysis were done. Bone mineral density (BMD) was measured with Piximus (GE Lunar Co. USA). The average values of these three methods were compared with each group. Results: After 6 weeks the BMD of the OVX group showed lower tendency than that of sham group. After 6 weeks many 3D parameters of micro-CT showed higher values in the OVX-alendronate group compared with the OVXsaline group. Most 2D bony parameters were higher in the OVX-alendronate group compared with the OVX-saline group at 9 weeks. Conclusion: This study showed low BMD of the OVX group after 6 weeks and showed the effect of alendronate on the BMD and bony structures of ovariectomized rats. This study also showed usefulness of in vivo micro-CT in monitoring individual bone changes over time.