Mechanisms for the incorporation of carbonate into minerals of the apatite group have been explored in both the geological and medical literature. An important problem with respect to biological apatite, which requires further clarification, is the hydroxyl content of the carbonated apatite of bone. Recent studies reveal bone apatite to contain only ~20 mol.% of the hydroxyl content of stoichiometric hydroxylapatite, with negligible chloride or fluoride. We investigated the hypothesis that the development of vacancies in the hydroxyl channel sites is a charge-balancing mechanism for the substitution of carbonate ions into hydroxylapatite. Raman spectroscopic analyses of synthetic carbonated apatites (containing 1 to >15 wt.% carbonate) show that their hydroxyl ion concentration correlates inversely with carbonate concentration. The specific relationship between carbonate and hydroxyl concentration in these samples closely follows the theoretical relationship defined by type-B substitution of carbonate for phosphate in the apatite structure. However, the 6–8 wt.% carbonate concentration in bone apatite falls far short of accounting for all of the hydroxyl depletion that occurs in bone apatite. Some of the additional hydroxyl depletion in bone apatite might result from substitution of Na+ for Ca2+, but further mechanism(s), perhaps (HPO4)2− substitution, must also play a significant role.