Bone mineral density (BMD) is known to vary based on various factors, and the degree of variation is site‐specific. However, few studies have investigated the relationship between bone density at trabecular bone‐rich and cortical bone‐rich sites in the same individual. In this study, we attempted to measure BMD at multiple sites using whole‐body computed tomography images taken immediately after death and to clarify the similarities and differences between skeletal sites. Additionally, we aimed to examine the factors that influence changes in BMD, such as the loading environment, bone microstructure, and the ossification process of each skeletal region. A 3D model containing BMD data of the skull, clavicle, lumbar vertebrae, and femur (neck and diaphysis) was created using computed tomography images taken immediately after the death of 60 individuals (28 men and 32 women, average age: 84.0 years) who consented to participate in the study before death. Arbitrary measurement sites were defined, and bone density was measured at each site. We found that the BMDs of all regions were negatively correlated with age, but this correlation was weaker in the skull than in other regions. The negative correlation was especially pronounced in areas with more trabecular bones in men and in areas with more cortical bones in women. Furthermore, these findings suggest that factors, such as the loading environment, bone microstructure, and the ossification process of the skeletal sites, affect the BMD. Furthermore, our results suggest that it is important to assess the BMD of cortical bone in older women.