Bone mineral density (BMD) measurements are critical in many research studies investigating skeletal integrity. For pre-clinical research, micro-computed tomography (μCT) has become an essential tool in these studies. However, the ability to measure the BMD directly from μCT images can be biased by artifacts, such as beam hardening, in the image. This three-part study was designed to understand how the image acquisition process can affect the resulting BMD measurements and to verify that the BMD measurements are accurate. In the first part of this study, the effect of beam hardening-induced cupping artifacts on BMD measurements was examined. In the second part of this study, the number of bones in the X-ray path and the sampling process during scanning was examined. In the third part of this study, μCT-based BMD measurements were compared with ash weights to verify the accuracy of the measurements. The results indicate that beam hardening artifacts of up to 32.6% can occur in sample sizes of interest in studies investigating mineralized tissue and affect mineral density measurements. Beam filtration can be used to minimize these artifacts. The results also indicate that, for murine femora, the scan setup can impact densitometry measurements for both cortical and trabecular bone and morphologic measurements of trabecular bone. Last, when a scan setup that minimized all of these artifacts was used, the μCT-based measurements correlated well with ash weight measurements (R² = 0.983 when air was excluded), indicating that μCT can be an accurate tool for murine bone densitometry.