Current levels of vitamin D (vit D) and calcium (Ca) in the reference AIN-93G rodent diet may be higher than required for healthy bone structure and bone mineral density (BMD). Other studies suggest that intestinal integrity may be altered by lowering levels of vit D or Ca. The study objective was to determine if lower diet levels of Ca and vit D support development of healthy bone structure and BMD in female CD-1 mice at 2 and 4 months of age without altering intestinal integrity. Lowering the levels of vit D (100 IU/kg) and Ca (3.5 g/kg) did not alter bone structure or BMD. Effects on intestinal integrity are less clear and requires further study using more comprehensive measures. Findings from this study suggest that dietary Ca and/or vit D at current levels in the AIN93G reference diet may mask potential benefits of nutritional interventions aimed at promoting bone health.