Waste materials from natural sources are important resources for extraction and recovery of valuable compounds. Transformation of these waste materials into valuable materials requires specific techniques and approaches. Hydroxyapatite (HAp) is a biomaterial that can be extracted from natural wastes. HAp has been widely used in biomedical applications owing to its excellent bioactivity, high biocompatibility, and excellent osteoconduction characteristics. Thus, HAp is gaining prominence for applications as orthopaedic implants and dental materials. This review summarizes some of the recent methods for extraction of HAp from natural sources including mammalian, aquatic or marine sources, shell sources, plants and algae, and from mineral sources. The extraction methods used to obtain hydroxyapatite are also described. The effect of extraction process and natural waste source on the critical properties of the HAp such as Ca/P ratio, crystallinity and phase assemblage, particle sizes, and morphology are discussed herein.