This study aimed at preparing and characterizing fluor-hydroxyapatite (FHA) nanocrystals using the sol-gel process. Phosphorus pentoxide, calcium nitrate, and hexafluoro acid were used as the sources of phosphorus, calcium, and fluorine to achieve the stochiometric ratio of 5 for calcium to fluorine, and 1.67 for calcium to phosphorus, respectively. In order to characterize and evaluate the properties of the particles, methods of elemental analysis (XRF), phase analysis (XRD), fourier transform infrared spectroscopy (FTIR), scanning electron microscope (SEM), and transmission electron microscope (TEM) were applied. The elemental analysis showed that the required oxides and elements deos exist in the compound in desired amounts. The results of XRD confirmed the structure of fluorapatite. The sizes of the crystallites estimated from XRD patterns using the Scherrer equation was about 40 nm. FTIR analysis proved the partial substitution of ion F with OH and the formation of fluorapatite. SEM and TEM images showed that the fluorapatite nanoparticles less than 50 nm were formed having spherical shapes. The results indicated that it is possible to prepare fluor-hydroxy apatite nanocrystals with desired composition and structure through sol-gel method.