In vivo micro-computed tomography (micro-CT) represents an advancement in assessing three-dimensional micro-architecture of bone in mouse models of osteoporosis by permitting longitudinal measurement of the same living animal over time. Repeatability of the measurement and analysis techniques and the effects of repeated radiation exposure on bone architecture are examined. The use of an in vivo protocol for mice is demonstrated by examining time-based skeletal response to ovariectomy in different inbred mouse strains. Typical morphological measurements in mice had less than 5% precision error. Repeatedly radiated limbs had 8-20% less bone volume than non-radiated limbs. Rate and extent of bone loss due to ovariectomy differed among inbred strains of mice, with higher bone mass strains losing more bone but maintaining higher overall bone volume levels. In vivo micro-CT offers new insight into time-based skeletal adaptation and will play an important role in future studies of bone health.