Much still remains unclear about the proximal biochemical effects of mutations on development of the phenotype in inborn errors of metabolism. Cystinosis is an example of this phenomenon. We have recently shown that cystinotic cells undergo apoptosis at a two- to fourfold higher rate than controls. Cystinotic cells pre-treated with cysteamine, normalizing cystine content, display a four- to fivefold decrease in apoptosis, while normal cells pre-treated with cystine dimethylester, increasing lysosomal cystine, exhibit a fivefold increase in apoptosis. We speculate that cystine exits the lysosomal compartment during early apoptosis and affects apoptotic proteins in the cytosol, causing an inappropriate commitment to proceed to cell death. The resulting chronic hypocellularity could account for all the characteristics of the nephropathic cystinotic phenotype. The milder variants of cystinosis may result from modifying mutations within an apoptotic protein, ablating the proapoptotic effects of cystine. Failure of the mouse knockout for cystinosis to show renal involvement may be the result of differences in apoptotic processes between man and mouse. Apoptosis is a major final common pathway for many disease states. Therefore, a better understanding of the effect of lysosomal cystine on apoptosis may help to clarify development of other diseases.