Anogenital warts are caused by human papillomavirus (HPV), over 30 types of which are infectious for the anogenital tract. Without treatment, warts may regress spontaneously, remain unchanged, or increase in number and size. This study compared the efficacy of a topical 5% potassium hydroxide (KOH) solution with that of a topical 0.5% 5-fluorouracil (5-FU) and 10% salicylic acid (SA) combination in the treatment of anogenital warts. Sixty patients were randomly assigned to receive topical KOH or 5-FU + SA. Both groups demonstrated a significant decrease in numbers of lesions (P < 0.05), but this difference was not significant at week 12 (P > 0.05). The mean number of lesions decreased from baseline to week 12 from 17.03 +/- 12.64 to 3.73 +/- 7.30 and from 16.13 +/- 12.97 to 3.10 +/- 4.90 in the KOH and 5-FU + SA groups, respectively (P < 0.001). Excellent clearance was achieved by 70.0 and 76.7% of patients in the KOH and 5-FU + SA groups, respectively. Marked improvement was seen in 13.3 and 20.0% of patients in the KOH and 5-FU + SA groups, respectively. At week 16, relapse was observed in two patients in the KOH group and three in the 5-FU + SA group (P > 0.05). No serious adverse events were reported. Neither treatment was more efficacious. Safety and ease of application are important goals in treatments for anogenital warts. A 5% KOH solution is a promising alternative treatment because it is effective and inexpensive and causes minimal side effects.