Aluminum (Al) is a trace element found in hard tissues, and the induction of bone diseases by Al accumulation has generated interest in the role and mechanism of Al in bone metabolism. Because hydroxyapatite (HA) constitutes the main inorganic content of human hard tissues, the biological effect of Al in human hard tissues is closely related to the intrinsic state of Al-doped HA (Al-HA). However, few investigations to date have focused on the crystallography of Al-HA. Herein, we determined the crystallographic characteristics and energy states of Al-HA by conducting theoretical and experimental studies. Al-HA [Ca10-1.5xAlx(PO4)(6)(OH)(2)] with a defect structure was synthesized. XRD patterns and morphology images revealed that doping of Al decreased the crystallinity and the HA nanocrystal size. The optimized crystal structure indicated that Al was preferentially substituted for Ca(2) and Ca vacancies appeared at the Ca(2)(1) site. Al doping locally distorted the regularity and integrity of the HA crystal structure, leading to the occurrence of Ca2+ vacancies and the displacement and rotation of OH- and [PO4](3-) chains. The total energy of Al-HA increased and the stability decreased. Consequently, Al-HA might be readily degraded by osteoclasts and bone resorption could be accelerated. The destruction and over-resorption of bones caused by excessive Al could result in abnormal bone metabolism. The present findings not only provide the first crystallographic information on the disruptive effects of Al doping in HA but also complement the present understanding of the mechanisms underlying Al-induced bone diseases.