Our understanding of the molecular basis of cystinuria has deepened as the result of the causative genes, SLC3A1 and SLC7A9, being identified. The proteins coded for by these genes form a heterodimer responsible for reabsorption of filtered cystine in the proximal tubule. Failure of this transport system to be targeted to the apical membrane, as in the case of SLC3A1 mutations, or failure of the transport system to function, as in the case of SLC7A9 mutations, leads to abnormal urinary excretion of the relatively insoluble amino acid cystine. Stones and plugs of tubules result, with chronic kidney disease a frequent complication. Here we review the genetics, pathophysiology, pathology, clinical manifestations and clinical management. Increased fluid intake, restriction of sodium and animal protein ingestion, and urinary alkalinization are the standard therapies. Cystine binding thiol drugs tiopronin and D-penicillamine are reserved for patients for whom the conservative therapies are insufficient. New studies of cystine crystal inhibition are highlighted.