Some carbonate apatites were investigated by computer simulation using the General Utility Lattice Program (GULP) with grid techniques. These structures were modeled by a semiempiric method using interatomic potential-based simulation techniques. The supercells of 3 × 3 × 3 elementary cells of carbonate apatite were considered. The arrangement of structural defects (carbonate groups, excess Fx ions, Na ions, Ca vacancies, hydroxyl groups, water molecules H2Ostr fixed in structure) in carbonate fluorapatite (CFA) with the chemical composition near to the synthesized A-B type CFA (2.7 wt% CO2, 3.3 wt% F) was established. Structural changes in the A type carbonate hydroxylapatite (CHA) due to formation of the CO2−-radical from the carbonate ion replaced two adjacent hydroxyls in the hydroxylapatite (HA) channel have been studied. The CO2−-radical formation is accompanied by the appearance of a Ca2 vacancy and results in the considerable rearrangement of ions of the structural environment. The anneal effect on the A type CHA structure with the CO2−-radical (CHAr) and possible accompanying defects has been investigated. The CHAr structure is most stable at the temperatures of T = 298 and 873 K; the CHA structure with the CO2−-radical and O−-center spaced by one hydroxyl in the same channel (CHAr–h–r) — at T = 1073 and 1173 K. The obtained data complement and are partly in agreement with experimental and theoretical investigations of CHA.