The formation process of inorganic crystals in biological systems (biomineralization) is the fruitage of an extended period of fine-tuning by evolution and is replete with material scientific key considerations. In this article, our recent attempts to elucidate the mineralization mechanism of hydroxyapatite (HAp) in natural bodies are described. It has been known that inorganic crystals precipitate onto organic matrix surfaces in biomineralization processes. Amphiphilic organic molecules assembled to monolayer films were employed to reproduce the organic matrices and the HAp precipitation process onto the monolayers were subjected to spectroscopic and structural analyses. We also determined the interfacial atomic structure of HAp {100} facet by using high-resolution transmission electron microscopy. A mechanism of HAp mineralization was proposed in view of the experimental results to determine the underlying reasons for refinement in structures of biominerals.