The aim of this paper is to present a protocol for the routine morphocompositional study of kidney stones in a clinical setting, and to demonstrate that it is a simple and useful approach that can reliably determine the etiology of all types of kidney stones. Our routine study of kidney stones consists of a combination of stereoscopic microscopy, scanning electron microscopy, and infrared spectroscopy. The usefulness of such a procedure is demonstrated by its application to several illustrating examples. The protocol applied here is reliable and fast, and does not require multiple infrared spectroscopic analyses for most non-homogeneous samples. It also provides the identification of components that are present in very small proportions, the characteristics of internal and external structures, and information about areas with biological structures, such as renal tubules. It should be noted that results are obtained in a relatively short time and with high reliability. The detailed morphocompositional study of a urinary calculus is essential for establishing the diagnosis and etiology and for initiating the treatment of a patient with renal lithiasis, because there is a relationship between the specific characteristics of a stone and the specific etiology of the disease. The increasing number of treatments available for patients with different types of renal calculi makes improvements in diagnosis and determination of stone etiology, such as the procedure described here, more important now than ever.