Background: Human papillomavirus (HPV)-induced lesions rarely develop in the urethral meatus (UM); however, their eradication can be problematic. Methods: A total of 22 patients with anogenital warts (AGWs) in the UM region and 22 patients with AGWs located at other anatomical sites were included in this cross-sectional study. The presence of human papillomavirus (HPV) types in biopsy samples was determined using the HPV Easy typing kit (GenID GmbH, Germany). Results: Although the patients in the AGW group with involvement of the UM had a higher incidence of reported multiple sexual partners (63.6% vs. 40.9%), larger meatus size (81.8% vs. 36.4%), and more frequent anal (36.4% vs. 18.2%) or unprotected sexual contact (68.2% vs. 36.4%) than those in the AGW group without UM involvement, only the duration of lesions (p = 0.04) and meatus size (p = 0.004) were significantly different in both groups. Low-risk HPV types were found in 75.0% and 69.2% of patients in the AGW groups with and without UM involvement, respectively. Conclusion: We found that a larger UM size was more prone to the development of meatus AGWs; however, being married, delaying sexual debut, and avoidance of multiple sexual partners seemed to be associated with a decreased risk of development of AGWs, especially within the UM region.