The purpose of the present cohort study was a quantitative assessment of the enamel, dentin, and alveolar bone mineral density (BMD) using Cone Beam Computed Tomography (CBCT) scans in patients with X-linked hypophosphatemic rickets (HLHR) and hypophosphatasia (HPP) and a comparison with the data obtained from the control group. Methods and Results: The unrepresentative, non-random sample included 30 CBCT scans of children with genetically and biochemically confirmed XLHR (OMIM #307800) and HPP (OMIM: 146300, 241510, 241500, and 146300). X-ray examination and dental care were carried out in the Radiology Diagnostics Department and Pediatric Dentistry Department at Moscow State University of Medicine and Dentistry named after AI Evdokimov. The mineral density of calcified tissues (enamel, dentin, and alveolar bone) was evaluated using i-CAT Vision TM software options on reconstructed CBCT axial views. The images of all XLHR and HPP patients visualized large pulp chambers with prominent pulp horns extending to the dentin-enamel junction. The present study revealed poor alveolar bone mineralization in patients with HPP and XLHR. Analysis of CBCT scans showed a significant dentine hypodensity in XLHR patients, which may contribute to the emergence of multiple, spontaneous, periapical abscesses spreading rapidly in the jawbone. Conclusion: Data obtained could be used for planning dental treatment of patients with XLHR and HPP.