Background and Objective: Genital warts, the most common sexually transmitted disease (STD), are caused by human papillomavirus (HPV). Few studies have been performed on Iranian women with genital warts or cervix cancer but there isno documented data about genital warts and HPV genotyping in Iranian men. In this study, we determined HPV genotypesin 108 male and females with anogenital warts in an STD clinic in Tehran.Methods: In this cross sectional study, HPV genotypes were determined by the PCR method in 108 males and females withanogenital warts who were visited at an STD clinic in Tehran within January–June 2012. Age, sex, number of sexual partners,education level, and marital status were recorded in the questionnaires.Results: We determined HPV genotypes in 108 patients including 36 men and 72 women. The mean age of the patients was 31.5±12.3 years. The most common type was type 6 (62%). Other common genotypes were 11 (28.7%), 18 (15.7%), 16 (14.8%), 31 (4.6%), 33 (0.9%), 51 (0.9%), 56 (0.9%), and 66 (0.09%). We found that genotypes 16 (P=0.003) and 31 (P=0.013) were more prevalent in the patients with a higher number of sexual partners. In addition, there was a statistically significant association between the number of sexual partners and multi type HPV infection (P=0.045). Genotypes 16 (P=0.036) and 11 (P=0.039) were significantly associated with the female gender.Conclusion: Our results showed that HPV 6 was the most prevalent HPV type followed by HPV 11, 18, and 16.