Because of the destructive nature of techniques used to measure bone morphometry, studies of architectural changes and bone loss have utilized cross-sectional study designs, with all its inherent limitations in nuances. Here, the results of a longitudinal study using in vivo micro-CT are presented elucidating the dynamics of bone loss and architectural adaptation in rat models of aging and postmenopausal bone loss. Using 3-D methodology, we observed the changes in bone architecture in the proximal tibia of normally aging and ovariectomized rats for 54 weeks. Spatial patterns in bone resorption were observed that were similar for both groups. Remaining trabeculae increased in thickness or were remodeled into new trabecular structures, especially in the ovariectomized animals. The combination of bone loss and bone formation resulted in alignment of trabeculae across the growth plate. Cortical modeling that was associated with growth continued after cessation of longitudinal growth in the ovariectomized animals, resulting in shape changes of the proximal tibia. The organized nature of the changes in bone architecture that occurred after ovariectomy and the high similarity with the changes observed in the normally aging animals, suggest that estrogen depletion resulted in an acceleration of a normal bone adaptation process. The observed aligning of trabeculae suggests regulation through mechanical loading.