Contrast agent enhanced cone beam computed tomography (CE-CBCT), a technique capable of high-resolution in vivo imaging with small radiation dose, has been applied successfully for clinical diagnostics of cartilage degeneration, i.e., osteoarthritis (OA). As an X-ray technique, CE-CBCT may also detect changes in mineral density of subchondral bone (volumetric bone mineral density, vBMD), known to be characteristic for OA. However, its feasibility for density measurements is not clear due to limited signal-to-noise ratio and contrast of CBCT images. In the present study, we created clinically applicable hydroxyapatite phantoms and determined vBMDs of cortical bone, trabecular bone, subchondral trabecular bone and subchondral plate of 10 cadaver (ex vivo) and 10 volunteer (in vivo) distal femora using a clinical CBCT scanner, and for reference, also using a conventional CT scanner. Our results indicated strong linear correlations between the vBMD values measured with the CT and CBCT scanners , however, absolute vBMD values were dependent on the scanner in use. Further, the differences between the vBMDs of cortical bone, trabecular bone and subchondral bone were similar and independent of the scanner. The present results indicate that vBMD values might not be directly comparable between different instruments. However, based on our present and previous results, we propose that, for OA diagnostics, clinical CBCT enables not only quantitative analysis of articular cartilage but also subchondral bone vBMD. Quantitative information on both cartilage and subchondral bone could be beneficial in OA diagnostics.