Using electron microprobe analysis, 17 kidney stones containing apatite were studied. According to the results of the research, it was found that the apatite of all the oxalate kidney stones contained fluorine, while in the apatite of the phosphate kidney stones, fluorine was present in trace amounts or absent. Direct correlation between the amount of oxalate mineral phases and the fluorine content was observed. Ionic substitutions in the apatite of kidney stones have a multidirectional effect on the unit cell parameters. The fluorine content increases with the increase of a unit cell parameter, which is probably associated with a simultaneous increase in the amount of H₂O in the structure of apatite. The results of thermodynamic modeling show that fluorapatite is stable at lower pH values than hydroxylapatite, and therefore can be a precursor of calcium oxalates crystallization.