We report a case of aphallia in a male neonate. The phallus was completely absent. The urethral meatus was located between the well developed bifid scrotum containing normal testes. Voiding cystourethrography revealed grade II VUR on the right side. The karyotype was 46XY. Other urogenital anomalies were not detected. Bilateral orchiectomy was performed at 2 months of age. The sex assignment and management of aphallia were discussed.