The waste from fish processing after the fish have been filleted can account for as much as 70 percent of the total catch weight. About 30 percent of such waste consists of scale and bone. This waste contains numerous valuable organic and inorganic components such as collagen and hydroxyapatite (HA), which have commercial value for use in manufacturing functional foods, cosmetics, and biomedical products. In particular, HA has been widely used as a biocompatible ceramic but mainly for contact with bone tissue, due to its resemblance to mineral bone. In this study, the authors have reviewed the characterization and applications of HA extracted from fish scale and bone. Moreover, several HA-based highly porous composite materials used for bone tissue engineering were also presented. Finally, a summary of HA preparation, characterization and applications will be given, together with the perspectives on this field of research.