Background: Bone, dentin, and enamel are tissues formed through calcification, a process involving deposition of calcium phosphate minerals on extracellular organic matrices. Calcification, the underlying mechanism of which is unknown, is initiated with mineral deposition followed by advancing of the deposit and subsequent maturation of the mineral crystal. Highlight: We have reviewed the current knowledge of how calcification proceeds during bone development, bone healing, and enamel and dentin development, based on reported studies. Previous studies reported by us and by other authors have suggested that degradation of some extracellular matrix (ECM) proteins is involved in calcification during bone and dentin development and bone healing in a manner similar to that previously reported for enamel development. Conclusion: The ECM proteins may inhibit mineral deposition and calcification, similar to the role of amelogenin during enamel development. The candidates for the amelogenin equivalents in bone and dentin have not been identified. Further studies are required to elucidate the regulatory mechanisms of bone and dentin calcification in light of specific ECM proteins that prevent calcification and enzymes that degrade these ECM proteins.