Background: Due to the reduction in HIV transmission through male medical circumcisions (MMC), numerous clinics throughout South Africa offer a voluntary free service to boys from the age of ten years and above. An examination prior to the procedure may detect congenital abnormalities missed after birth. Objectives: The aim of this study was to measure the incidence of these abnormalities, determine the demographic and clinical characteristics of this group and determine what referral systems, interventions, and follow-up is available to them. Methods: The study was a descriptive, observational, retrospective analysis of de-identified medical records at a routine MMC service at a Johannesburg clinic in 2015. The participants were male patients between the ages of 10 – 49. Results: Out of 1548 participants, 91.0% (n=1409) had a normal genital examination while 3.7% (n=57) had an abnormal examination and 5.1% (n=79) had no examination recorded. Thirty five congenital anomalies were detected and only 2 patients (diagnosed with hypospadias) were seen at the urology out-patient’s department. Conclusion: The incidence of congenital genital abnormalities of males presenting for routine circumcision is low. Despite the low incidence the effect on fertility, sexuality, ability to urinate and on psychological wellbeing is significant. Referral services to the urology department should be restructured to improve all outcomes.