Cystinosis is a rare genetic disease characterized by defective lysosomal cystine transport and increased lysosomal cystine. How lysosomal cystine causes the lethal nephropathic phenotype is unknown. It was shown recently that cultured fibroblasts and renal proximal tubule epithelial cells whose lysosomes are cystine-loaded display a two-fold or greater increase in apoptosis after both intrinsic and extrinsic stimuli. The mechanism for the increased apoptosis is unknown. Protein kinase C␦ (PKC␦) is a proapoptotic protein kinase that has been shown in vitro to be activated via cysteinylation. This report now shows that PKC␦ forms disulfide bonds specifically with cystine that is released from lysosomes in cultured fibroblasts and renal proximal tubule epithelial cells during apoptosis. PKC␦ in cystinotic fibroblasts and renal proximal tubule epithelial cells have a four-to six-fold greater association with its substrate, lamin B, and a 2.5-fold increase in specific activity after TNF-␣ exposure. Both RNA inhibition and chemical inhibition of PKC␦ resulted in a significant decrease in apoptosis in cystinotic cells but not in normal cells. It is proposed that abnormally increased apoptosis plays a role in evolution of the cystinotic phenotype.