This study compared percutaneous sclerotherapy using 50% acetic acid with that using 99% ethanol for patients with simple renal cysts. The study included 72 simple renal cysts in 64 patients (male/female ratio = 31/33; age range, 31-75 years). Under fluoroscopic guidance, the cyst fluid was aspirated completely. Sclerotherapy was then performed using 50% acetic acid for 32 cysts and 99% ethanol for 40 cysts. The volumes of each renal cyst before and after sclerotherapy were compared using ultrasonography or CT. Medical records were reviewed to analyse any complications. The mean follow-up period was 21.5 months (range, 3-75 months). The mean remnant volume of the cyst after sclerotherapy was 2.6% of the initial volume in the acetic acid group and 14.0% in the ethanol group. The rates of complete remission, partial remission and treatment failure were 90.6%, 9.4% and 0%, respectively, in the acetic acid group, and 60.0%, 30.0% and 10.0%, respectively, in the ethanol group. There were no complications related to sclerotherapy in either group. In conclusion, acetic acid is a safe and effective sclerosing agent, with clinical results superior to those of ethanol, and is an alternative to ethanol for sclerotherapy of renal cysts.