Renal calculi samples were investigated with synchrotron radiation based microtomography on the resolution level of few microns. XRF and XRD were used in order to investigate samples composition. The histograms of the 3D stone images were analyzed by fitting set of Gaussian functions. The assumption that every stone compound gives additional maximum to the histogram allowed the identification of some pattern compounds. The compounds usually present in renal stones were considered. The results of XRD and histogram findings correlate well. Advantage of proposed method relies on the possibility of calcium oxalates differentiating, differentiating of more compounds than XRD without additional effort and gives perspective to the quantitative analysis of different compounds amounts in the studied samples.