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Introduction Cervical cancer is the fourth most common cancer in females demonstrating approximately more than 7% of all woman cancer mortality in 2018. HPV infection considered as the pivotal risk factor for cervical cancer induction. Permanent infection with carcinogenic genital HPVs increases the predisposition of cervical cancer. In this study, we investigated the frequency of HPV genotypes in a sample of Iranian population. Methods Therefore, 2135 individuals with genital warts between 2015 and 2018 recruited to the study. After DNA extraction, PCR amplification and genotyping were employed by HPV Direct Flow CHIP Kit and the e-BRID System®, supported by hybriSoft ™. HPV was found in 92% of the samples obtained from the patients. Results In total, 12.6% and 87.4% of warts were positive for any high-risk and low-risk genotypes, respectively. HPV 16 and 6 were the most predominant HR and LR genotypes in all categorized age groups (5.26% and 40.71%, respectively). Moreover, by getting older, the frequency of HPV 6 was decreased (P = 0 .018, r = −0.050) and the frequency of HPV 56 was increased (P =0 .026, r = 0.044). Conclusion Although we noticed lower prevalence of high risk HPV particularly 16 and 18 in genital warts in the East of Iran; however, genotyping of genital warts still recommended.