Penile agenesis is one of the rarest urogenital anomalies with only less than 100 cases reported worldwide so far. Only 3 cases have been reported from Africa and to our knowledge none has been reported from our country Ethiopia. Viability depends on associated anomalies. Urogenital anomalies are the most common associated ones accounting for 54% of cases. This case report is unusual presentation, which is the first reported case of penile agenesis associated with left to right, crossed fused renal ectopia.