Urolithiasis is one of the major health issue in urinary system which causes large health care burden. Although many therapeutic options have been develop for the treatments of renal stones, mechanism of formation of renal stone is still remains as controversial. In order to detect formation of stone in different anatomical locations in renal system, we have examined 76 renal stone samples in different anatomical locations collected from Teaching Hospital, Peradeniya. Surface and cross sectional visual and microscopic analysis were done in all samples. Advanced morphological data and photographs were obtained through polarizing microscope using plane and crossed polarized light. Serial chemical characterization was carried out by using on X-ray Fluorescence (XRF) Spectrometer (Fisher-Scope XAN). From that study we found to have that the nucleation is the most important step for the formation of urinary calculi and it could be the organic matter. Also, the fragments of early formed stones within pelvicalyceal system could also be the nuclei of stones of other anatomical location. Nucleus and periphery have two different lamination patterns in polarized light and morphological and chemical data indicates significant difference between nucleus and periphery of a renal stone. It clearly shows that formation of nucleus and periphery of a stone is governed by two different processes. Based on these data urinary calculi can be differentiated according to their origin and growth. Also it may help to modify the correct treatment of urinary calculi.