We have synthesized large chlorapatite [ClAp, Ca(5)(PO(4))(3)Cl(x)(OH)(1-x), where x = 1] single crystals using the molten salt method. We have corroborated that the hexagonal symmetry P6(3)/m describes the crystal structure best, even though the crystals are synthetic and stoichiometric. Moreover, we have performed several thermal treatments on these ClAp crystals, generating new single crystals in the apatite system [Ca(5)(PO(4))(3)Cl(x)(OH)(1-x), where x ≤ 1], where the chloride anions (Cl(-)) were systematically substituted by hydroxyl anions (OH(-)). These new single crystals were methodically characterized by powder and single-crystal X-ray diffraction (SXRD), scanning electron microscopy (SEM), Fourier transform-IR spectroscopy (FT-IR), and energy-dispersive X-ray spectroscopy (EDS). We have discovered a previously unreported OH(-) inclusion site substituting the Cl(-) anion during the ion-exchanging process. Finally, we evaluated the atomic rearrangements of the other species involved in the structure. These movements are associated with ionic exchange, which can be justified from an energetic point of view. We also found a novel phase transformation at high temperature. When the crystals are heated over 1753 K the apatite system evolves to a less ordered monoclinic structure, in which the complete loss of the species in the anionic channel (Cl(-), OH(-)) has been confirmed.