The effects of physical activity and dietary calcium on bone development are not fully understood. Forty-nine female, B6 mice were either given access to a running wheel or housed in a limited activity environment and either fed a regular calcium diet (0.95% Ca) or high calcium diet (2.0% Ca) at 4 weeks of age. These mice were sacrificed at age 16 weeks and their lumbar vertebrae and femurs were measured by micro-CT. High calcium mice exhibited higher values in trabecular and cortical bone traits in both the femur and vertebra than did regular calcium mice. Running had little impact on bone in this study and the independent effects of the high calcium diet outweighed those of running. In conclusion, increased calcium intake was more beneficial than running in developing bones and running does not seem to represent effective therapy for bone improvement during development.