With an incidence of 1:7000 births, cystinuria, the most frequent cause of stone formation among genetic diseases, represents a major medical problem. Twentyfive cystine stones randomly selected from cystinuric patients were investigated. From a crystallographic point of view, cystine stones are composed of micrometre size crystallites, which are made up of an aggregation of nanocrystals. Through scanning electron microscopy, the morphology and size of the crystallites have been described, while the size of the nanocrystals was investigated by means of powder neutron diffraction. Powder neutron diffraction analysis and/or scanning electron microscopy examination of cystine stones provide evidence that usual alkalinization by sodium bicarbonate associated with high diuresis significantly reduces the size of both nanocrystals and crystallites, while for other treatments, including alkalinizing drugs and thiol derivatives, the data suggest mainly changes in the topology of crystallites. Alkalinization with sodium bicarbonate affects cystine kidney stones at the mesoscopic and nanoscopic scales, while other medical treatments only alter their surface. Such an approach may help to assess the interaction between drugs and cystine stones in cystinuric patients.