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This paper focuses on the study of the effect of the change of the crystal size on the shape and width of the X-ray diffraction patterns for defatted and deproteinized bones as well as incinerated biogenic hydroxyapatite obtained from bovine, porcine, and human bones. Inductively Couple Plasma showed the presence of some ions such as Mg, K, Al, Fe, Zn, and Na for all samples. The nanometric size of the crystals was determined through High Resolution Transmission Electron Microscopy in which ordered crystals were found. The calcination of raw clean bones at 720 °C produced a transition of crystal size from nano to micro due to a coalescence phenomenon, this was accompanied by a decrease of the peak width of the X-ray diffraction patterns due to the decrease of the inelastic scattering contribution from the microcrystals. A simulation of the effect of the crystallite size on the shape and width of the X-ray patterns was done using PDF-4 software which confirmed that raw ordered bone crystals produce broad peaks which so far have been erroneously assigned to polycrystalline hydroxyapatite with low crystalline quality.