Cystinosis, a rare autosomal recessive lysosomal storage disease, is due to impaired transport of cystine from lysosomes. The disease results in deposition of crystals throughout the body; if untreated, it leads to failure to thrive, profound metabolic imbalance, early end-stage renal disease, thyroid failure, and multiorgan dysfunction. As this review describes, substantial progress has been made in our understanding and treatment of this disorder. The administration of cysteamine, each molecule of which can combine with a half-molecule of cystine (cysteine) to facilitate the exit of cystine from the lysosome, has greatly improved the course of the disease. In addition, the gene for cystinosis, CTNS, which encodes a protein called cystinosin, was isolated in 1998, opening new avenues for understanding this condition.