Background: Cryotherapy is one of the most common and effective treatments of anogenital warts, and trichloroacetic acid is one of the methods commonly used. The aim of this study was to compare the effect of cryotherapy and trichloroacetic acid in the treatment of anogenital warts.Methods: This randomized clinical trial was conducted on patients with anogenital warts. The patients were divided into two groups; one group was treated with liquid nitrogen and theother with 70% trichloroacetic acid. In both groups, the treatment was done every two weeks until complete disappearance of the lesions or for 6 sessions.Results: In this study, 68 patients with anogenital warts were studied. After the 6th session, the cure rate of in the patients treated with trichloroacetic acid (94.1%) was higher than the patients treated with cryotherapy (85.3%) (P>0.05).Conclusion: It seems that cryotherapy and trichloroacetic acid therapy have similar results in the treatment of anogenital warts.