Although alterations in bone mineral density (BMD) at the proximal tibia have been suggested to play a role in various musculoskeletal conditions, their pathophysiological implications and their value as markers for diagnosis remain unclear. Improving our understanding of proximal tibial BMD requires novel tools for three-dimensional (3D) analysis of BMD distribution. Three-dimensional imaging is possible with computed tomography (CT), but computational anatomy algorithms are missing to standardize the quantification of 3D proximal tibial BMD, preventing distribution analyses. The objectives of this study were to develop and assess a registration method, suitable with routine knee CT scans, to allow the standardized quantification of 3D BMD distribution in the proximal tibia. Second, as an example of application, the study aimed to characterize the distribution of BMD below the tibial cartilages in healthy knees. A method was proposed to register both the surface (vertices) and the content (voxels) of proximal tibias. The method combines rigid transformations to account for differences in bone size and position in the scanner's field of view and to address inconsistencies in the portion of the tibial shaft included in routine CT scan, with a nonrigid transformation locally matching the proximal tibias. The method proved to be highly reproducible and provided a comprehensive description of the relationship between bone depth and BMD. Specifically it reported significantly higher BMD in the first 6 mm of bone than deeper in the proximal tibia. In conclusion, the proposed method offers promising possibilities to analyze BMD and other properties of the tibia in 3D.