We have attempted to use heat treatment followed by ultrasonic treatment to separate the apatite from the non-apatite components of bone mineral in samples from different animals. The Mg content and the Ca/P ratio in the temperature range 560°C–720°C in the samples before and after ultrasonic treatment were determined by electron-probe x-ray microanalysis. Furthermore, we used atomic absorption spectrometry to measure the Mg content in powdered bone samples only after annealing and in distilled water, which was the “sonication” medium. We obtained evidence for thermally activated transition of Mg from a structurally bound state to a labile state at 680°C–720°C. At the same temperature, the Ca-deficient apatite is transformed to stoichiometric apatite. The data presented are evidence that crystals of Ca-deficient bioapatite are surrounded by Ca-enriched surface layers. As a result of thermal transformations at 680°C-720°C, all the Mg in the biomineral is found in the non-apatite environment surrounding the crystals and is removed by ultrasonic treatment, while the surface-localized Ca penetrates into the apatite lattice, restoring its stoichiometry.