In the past, bone loss in the ovariectomized (OVX) osteoporotic rat model has been monitored using in vitro micro-computed tomography (micro-CT) to assess bone structure (bone volume/total volume, BV/TV). The purpose of this study was to assess the importance of baseline control and sham groups in 12-16-week-old, reproductively mature rats. Measurements were carried out in a longitudinal and age-matched fashion using newer in vivo peripheral quantitative computed tomography (pQCT), which measures apparent bone mineral density (BMD). BMD was measured at the distal femoral metaphysis of 12-week-old female Wistar rats with pQCT. Subsequently, animals were either OVX or sham operated, and pQCT measurements were repeated four weeks later. Then, all rats were euthanized and in vitro BMD and BV/TV were obtained by micro-CT imaging. Results from three consistently differentiated regions of interest showed that there was significant bone loss and growth during the four weeks in the OVX and sham group, respectively. Taking this into account, i.e. a posteriori superimposing growth to loss, no differences resulted between BMD values measured in a longitudinal fashion with pQCT and that measured in comparison with an age-matched sham group with micro-CT and pQCT. In addition, there was a strong linear correlation between BMD measured with pQCT and BV/TV obtained from micro-CT. In conclusion, this outcome provides new insights into individual bone changes due to OVX and growth in Wistar rats during the age period of 12-16 weeks, which is often applied in osteoporosis research as the 'mature' rat model. Data can be used as baseline information upon which future in vivo study designs with this rat model can refer to reduce and minimize animal use.