Circumcision is one of the commonly performed procedures on males in the United States, Canada, Australia, and the United Kingdom. The association of minor anatomic variations of the newborn genitalia in patients with minor circumcision complications has not been previously examined. In this study, we looked for an association between subtle genital anatomic variations and newborn circumcision complications.Over an 18-month period, children presenting for circumcision revision were examined for minor variations in genital anatomy. Children referred for other urological problems during the same period comprised the control group. The same physician evaluated all of the children.During this period, 68 children were evaluated for possible circumcision complications. A confirmed complication was present in 57 infants. Patients with a minor circumcision complication were found to have a 9-fold higher incidence of a prominent suprapubic fat pad, penoscrotal webbing, or being a premature infant as compared to the control group.Subtle anatomic variations may be associated with a higher incidence of circumcision complications. Physicians performing newborn circumcisions should thoroughly examine the genitalia for these anatomic variations prior to the procedure in order to reduce potential complications.