Biological apatites are characterised by various ionic substitutions within the HAp lattice that are crucial for bone metabolism. The introduction of key role elements within synthetic calcium phosphates (CaP), mainly hydroxyapatite (HAp), can increase osteogenesis and enhance bone regeneration process. The lattice structure of HAp enables cationic and anionic substitutions leading to the enhanced biological performance of synthetic bone graft materials. This review summarises recent and relevant studies on cationic and anionic substitutions in the HAp lattice that are commonly found in the human body. Furthermore, co-substituted HAp obtained from synthetic and biological precursors, along with their influence on the bone regeneration process, has been discussed. Finally, future perspectives for the use of substituted HAp have been presented.