The natural progression of nephropathic cystinosis to end stage renal disease can be delayed, sometimes by many years, by the reducing agent, cysteamine, which lowers intracellular cystine content to near normal. We report on two patients with nephropathic cystinosis who were treated with cysteamine and developed structural genitourinary abnormalities which may have contributed to an increase in the rate of decline of renal function. One patient, aged 11 years, was found to have massive megacystis and hydroureteronephrosis but no anatomic bladder outlet obstruction. His abnormality was presumed to be related to chronic high urine volumes leading to megacystis and physiologic ureteral obstruction. Vesicostomy stabilized renal function. The second patient, aged 11 1/2 years, was found to have bilateral renal cystic disease which presumably was acquired and may have been related to long-standing hypokalemia. Minor renal abnormalities were found by ultrasound in five additional cystinotic children. We concluded that older children with nephropathic cystinosis may be prone to acquire structural abnormalities of their kidneys or urinary tract.