The major manifestations of nephropathic cystinosis are renal tubular acidosis, vitamin D-resistant rickets, and dwarfism. Cystine crystals are deposited in a variety of cells, mainly phagocytic, including macrophages of the intestinal lamina propria. Previously, ultrastructural changes were suggested to occur in the absorptive epithelium as well, possibly as a result of local cystine toxicity. We report here on the light- and electron-microscopic findings in the jejunal mucosa of two patients, aged 4 and 9 years with nephropathic cystinosis. Cystine crystals were easily identified in semithin sections of plastic-embedded specimens as brick- and hexagon-shaped spaces in macrophages. Electron microscopy showed that all crystals were in single-membrane-limited bodies (lysosomes), within phagocytic cells, and exclusively located in the lamina propria. In contrast to previous findings, the absorptive epithelium showed no abnormalities. We conclude that the growth failure in cystinosis is not a consequence of morphological toxic alterations in the intestinal epithelium, but is related to the known metabolic abnormalities of this condition. The use of rectal suction biopsy as a means of diagnosing cystinosis is also suggested as an alternative to other diagnostic methods.