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Abstract Background Congenital prepubic sinus is a rare anomaly found in the midline of the lower abdomen. Congenital prepubic sinus is usually asymptomatic in neonates, and a diagnosis is often achieved later in life after spontaneous extrusion of purulent material from the pre-existing hole in the pubic region. We present a case of congenital prepubic sinus presenting with purulent discharge after circumcision. Case summary A 4-year-old Caucasian boy presented to our urology out-patient clinic with purulent discharge from the distal part of the dorsum of his penis. He had a history of circumcision performed at a different center, 6 months ago. His parents stated that although various antibiotics were used, the purulent discharge continued for 6 months and the child had no complaints before circumcision. His condition was reported as superficial dorsal venous thrombosis, known as penile Mondor disease, in magnetic resonance imaging that was performed in the previous hospital. A physical examination revealed a small pinhole lesion at the distal part of his penis and a rigid cylindrical tube extending to the proximal side of his penis. We performed fistulography by injecting contrast material through a small angiocatheter and confirmed the diagnosis of prepubic sinus. Surgical exploration was performed and a long sinus, apparently ending as a fibrous tract at the anterior surface of his pubic symphysis, was found and resected. Conclusions Before congenital prepubic sinus surgery, it is critically important to rule out penile Mondor disease and the possibility of a circumcision complication (especially infective complications) mimicking congenital prepubic sinus.