Recently developed in vivo animal high-resolution micro-CT scanners offer the possibility to monitor longitudinal changes in bone microstructure of small rodents, but may impose high radiation doses that could damage bone tissue. The goal of this study was to determine the effects on the bone of 8 weeks of in vivo scanning of the proximal tibia in female Wistar rats. Eight weekly CT scans were made of the right proximal tibia of nine female, 30-week-old, retired-breeder, Wistar rats. Two weeks after the last weekly scan, a final scan was made. The left leg was only scanned during first and final measurements and served as a control. A two-way ANOVA with repeated measures was performed on the first and last measurements of left and right tibiae for six bone structural parameters. Bone marrow cells were flushed out and tested for cell viability. No significant difference was found between left and right for any of the bone structural parameters (p > 0.05). Structure model index and trabecular separation significantly changed as a result of aging, while none of the other parameters did. No significant difference was found between left and right in absolute and percentage number of cell viability. We did not find any indication that the applied scanning regime, in combination with the particular settings used, would affect the results of in vivo bone structural measurements in long-term studies using aged, female Wistar rats. However, careful consideration should be made when determining the number of scans, particularly when a different experimental design is used.