Urinary calculi have been recognized as one of the most painful medical disorders. Tenable knowledge of the phase composition of the stones is very important to elucidate an underlying etiology of the stone disease. We report here the results of quantitative X-ray diffraction phase analysis performed on 278 kidney stones from the 275 patients treated at the Department of Urology of Hadassah Hebrew University Hospital (Jerusalem, Israel). Quantification of biominerals in multicomponent samples was performed using the normalized reference intensity ratio method. According to the observed phase compositions, all the tested stones were classified into five chemical groups: oxalates (43.2%), phosphates (7.7%), urates (10.3%), cystines (2.9%), and stones composed of a mixture of different minerals (35.9%). A detailed analysis of each allocated chemical group is presented along with the crystallite size calculations for all the observed crystalline phases. The obtained results have been compared with the published data originated from different geographical regions. Morphology and spatial distribution of the phases identified in the kidney stones were studied with scanning electron microscopy (SEM) and energy-dispersive X-ray spectroscopy (EDS). This type of detailed study of phase composition and structural characteristics of the kidney stones was performed in Israel for the first time.