Biological apatites composing the inorganic part of many hard tissues have many characteristics differing from mineral and/or synthetic apatites. Before the modern precise analytical technique and methods were introduced to the hard tissue study, the non-stoichiometry of biological apatites was a problem, and the carbonated apatite in bone and tooth was sometimes mistaken for a mixture of calcium carbonates, calcium phosphates, and calcium oxides. Apatite is a mineral group which makes wide ranged solid-solution systems. Although hydroxyapatite is the most stable phase in the mimetic conditions to body system among the calcium phosphates, it can not be successfully precipitated under laboratory conditions. Therefore, some mechanisms have been proposed to crystallize biological apatite in the body conditions. In this review, the history of unveiling the nature of biological apatites is described from a crystallographic viewpoint, and bio-medical applications of calcium phosphates are introduced.