OBJECTIVE It gives important information in selecting the appropriate treatment for urolithiasis to confirm the component of urinary calculus. Presently component analysis of the urinary calculus is generally performed by infrared spectroscopy which is employed by companies providing laboratory testing services in Japan. The infrared spectroscopy determines the molecular components from the absorption spectra in consequence of atomic vibrations. It has the drawback that an accurate crystal structure cannot be analyzed compared with the X-ray diffraction method which analyzes the crystal constituent based on the diffraction of X-rays on crystal lattice. The components of the urinary calculus including carbonate are carbonate apatite and calcium carbonate such as calcite. Although the latter is reported to be very rare component in human urinary calculus, the results by infrared spectroscopy often show that calcium carbonate is included in calculus. The infrared spectroscopy can confirm the existence of carbonate but cannot determine whether carbonate is originated from carbonate apatite or calcium carbonate. Thus, it is not clear whether calcium carbonate is included in human urinary calculus component in Japan. In this study, we examined human urinary calculus including carbonate by use of X-ray structural analysis in order to elucidate the origin of carbonate in human urinary calculus. METHODS We examined 17 human calculi which were reported to contain calcium carbonate by infrared spectroscopy performed in the clinical laboratory. Fifteen calculi were obtained from urinary tract, and two were from gall bladder. The stones were analyzed by X-ray powder method after crushed finely. RESULTS The reports from the clinical laboratory showed that all urinary culculi consisted of calcium carbonate and calcium phosphate, while the gallstones consisted of calcium carbonate. But the components of all urinary calculi were revealed to be carbonate apatite by X-ray diffraction. The components of gallstones were shown to be calcium carbonate (one calcite and the other aragonite) not only by infrared spectroscopy but by X-ray diffraction. CONCLUSIONS It was shown that component analysis of the calculus could be more accurately performed by adding X-ray diffraction method to infrared spectroscopy. It was shown that calcium carbonate existed in a gallstone. As for the carbonate in human urinary calculi, present study showed that it was not calcium carbonate origin but carbonate apatite origin.