As viral sexually transmitted infections (STIs) are hard to cure completely and because they recur frequently, the management of patients and the prevention of the spread of viral STIs are important, rather than focusing on their treatment, unlike the focus for bacterial STIs. Thus, their prevalence and epidemiological characteristics should be investigated first. This study examined the prevalence of genital herpes and condyloma acuminata in patients visiting urologic and gynecologic clinics and evaluated the epidemiological characteristics of these diseases through questionnaire surveys. Out of 167,767 patients, 1,585 were reported to have genital herpes and condyloma acuminata, and the prevalences of the two diseases were 0.58 and 0.37%, respectively. The percentage of patients with viral STIs as a proportion of the total number of patients with STIs including bacterial STIs, was 35.6%. While the prevalence of genital herpes was relatively higher in middle-aged patients, that of condyloma acuminata was observed to be higher in relatively young patients. Among the patients participating in the questionnaire survey, 39.5 and 21.0% responded that they had experienced recurrence of genital herpes and condyloma acuminata, respectively. In conclusion, because the prevalences of genital herpes and condyloma acuminata as viral STIs were not trivial compared to that of bacterial STIs, and because of their frequent recurrence, policies adjusted to the characteristics of these viral STIs and more studies on the management of recurrence are necessary.