Abstract A systematic study of defect constellations in calcium-deficient hydroxyapatite is reported. Along this line, we explore different arrangements for charge compensation, including cationic vacancies and substitutional defects. The overall defect constellation is governed by both the different proton affinity of the anions or energy costs related to vacancy formation and minimization of the Coulomb energy which implies small distances of the anionic and cationic defects. Depending on the type of the calcium-deficient site, this gives rise to two specific defect arrangements. Among these, the calcium ions forming triangles which embed the OH − ions of hydroxyapatite are most likely to be deficient. The resulting charge is compensated by protonation of the OH − ion within the deficient calcium-triangle and protonation of a PO 4 3− ion in the nearest neighbourhood of the vacant calcium site. The strong energetic favouring of such constellations indicates that the commonly used chemical formulae Ca 10− x (HPO 4) x (PO 4) 6− x (OH) 2− x (H 2O) x (0< x⩽1) reflect a reasonable approximation of the composition of calcium-deficient hydroxyapatite.