Among various biocompatible materials, hydroxyapatite (HA) is widely used in medical applications. Hydroxyapatite can be used as temporary substitute material for the human bone. Despite of the risk of contamination during milling, the mechanochemical method shows higher reproducibility and low processing cost. In this investigation, the mechanochemical method has been carried out to produce nanocrystalline powders of hydroxyapatite using two experimental procedures (HA1: CaHPO4 + Ca (OH) 2; HA2: CaCO3 + CaHPO4) in polymeric and metallic vials at different milling time. The Effects of milling time, milling media and also chemical composition of initial materials on the crystallinity and morphological properties of obtained materials using X-ray diffraction (XRD) and transmission electron microscopy (TEM) were studied. Appropriate equation and graphs for determining crystallinity degree were used. The obtained results show that the crystallites sizes are within the nanometer range and also indicated that nanocrystalline hydroxyapatite with spherical morphology and high crystallinity degree can be produced much better in polymeric vials; therefore using polymeric vials with high wear resistance can have better performance during the mechanochemical process for the production of high quality nanocrystalline hydroxyapatite. Further work is needed to expand the idea for mass production.