Various types of organic matrices from small molecules to large ones have been extracted, purified, and identified from various biominerals over 20 years by our research group. They do not necessarily have common chemical structures. Our experimental experiences on those organic matrices have brought a new idea that they are classified into three groups depending on stepwise extraction and their function. This idea may be applicable to almost all biominerals and contribute to depict the whole image of biomineralization. Another contribution to this research field is introduction of the methodology of bioactive substance chemistry, which resulted in the discovery of important functional organic matrices such as Pif, CMAP, CAP-1, PEP (phosphoenolpyruvate), and 3-PG (3-phosphoglucerate). Thus, the importance of organic matrices in biomineral formation was proved, and a new aspect in biomineralization research was explored.