Hydroxyapatite [Ca10(PO4)6(OH)2; HAp] is the mineral component of vertebrate hard tissues and an important raw material for biomaterials. The HAp crystal belongs to a hexagonal system and has two types of crystal plane with different atomic arrangements: positively charged calcium ions are mainly present in the a(b)-planes, while negatively charged phosphate ions and hydroxyl groups are mainly present in the c-planes. In vertebrate long bone surfaces, HAp crystals have a c-axis orientation, which leads to the development of the a(b)-plane; while in tooth enamel surfaces, they have an a(b)-axis orientation, which leads to the development of the c-plane. However, it is not clear why the orientations of long bone and tooth enamel are in different crystal planes. In order to clarify this question, we have synthesized single-crystal apatite particles with preferred orientation to the a- and c-axes as models for bone and teeth enamel. This review first describes the syntheses process of single-crystal apatite particles with preferred orientation to a(b)- and c-axes and then discusses specific protein adsorption to the crystal surface of the resulting plate- and fiber-shaped apatite particles with different surface charges. In addition, porous apatite-fiber scaffolds (AFSs) fabricated using the fiber-shaped apatite particles and their application to tissue engineering of bone are described on the basis of the three-dimensional cell culture of mesenchymal stem cells derived from rat bone marrow using the AFS settled into a radial-flow bioreactor.