National guidelines state that hepatitis B and C testing should be targeted to those with risk factors. However, there is little data to support this recommendation. There is also limited data of viral hepatitis prevalence in attendees at genitourinary medicine clinics. We report the prevalence of hepatitis B infection in an unselected genitourinary medicine population, and hepatitis C directed by risk assessment including all men who have sex with men. Routinely collected clinic data from statutory returns was combined with laboratory test result data. Clinical notes of those testing positive were reviewed to determine risk factors and HIV status. HBsAg was positive in 13 (0.2%) of 6020 patients and hepatitis C Ab/Ag in 12 (1.0%) of 1153. All patients who tested positive for viral hepatitis infection had risk factors that would have prompted testing under national guidelines. Five of the 12 with positive hepatitis C Ab/Ag (0.4% of those tested) tested positive for hepatitis C RNA, indicating current infection. The prevalence of hepatitis B and C were in line with previously published data. Our results do provide support for the basis of targeted testing for viral hepatitis, as stipulated in national guidelines, in that all patients testing positive had risk factors.