Bone has a well-organized microstructure at a nano-scale level and is composed of mineral apatite (Ap) and collagen (Col) fibril, providing reinforcement and pliability, respectively. Since Ap crystallizes under an anisotropic hexagonal lattice, the mechanical properties of an Ap crystallite are expected to depend on crystal orientation. The preferential alignment of the Ap c-axis along the extended collagen fibrils in bones depends strongly on the portion of bone. Therefore, new materials for bone replacement should possess the preferential alignment of Ap c-axis and Col fibril. In this study, we have developed Ap/Col composites with their preferential alignment on the basis of self-organization process by soaking a CaCl2/Tris-HCl buffer solution and a Na2HPO4 solution alternately (an alternate soaking process developed by Prof. M. Akashi). Deposition of Ap crystallites with preferential alignment of the c-axis was finally achieved in collagen matrix with preferred fibril direction.