Genital warts (GW) are mucosal or skin lesions caused by sexual transmission of human papillomavirus (HPV). This study estimates the frequency of GW cases in physicians’ clinics and physicians’ usual practices of GW referral and diagnosis in Peru. Participants in this study were a convenience sample of 100 physicians in five specialties: primary care (17), gynecology (37), urology (10), dermatology (31), and infectious diseases (5). Physicians completed a survey and daily log of all patients aged 18–60 years seen over ten days in their offices located in Peru. The survey recorded GW referral patterns and the daily log recorded patient demographic information and GW diagnosis. Among 12,058 patients, the annual GW prevalence (95% confidence interval [CI]) was 2.28% (2.02–2.56) and cumulative incidence (95% CI) was 1.60% (1.38–1.84). Physicians reported that most GW patients were direct consult (73.5% of male and 67.9% of females) and physicians treated most GW patients themselves (73.4% of males and 76.7% of females). As reported, the most common reasons for referring were ‘serious cases requiring more specialized treatment’ (73.2% of male and 72.2% of female) and ‘lack of resources to treat’ (26.8% of male and 27.8% of female). We conclude that GW cases are commonly seen by physicians in Peru.