BACKGROUND: Congenital aphalia is an extremely rare, urogenital malformation of the external genitalia characterized by congenitally absent penis in a karotypically XY child. It occurs 1 in 30 million live births.So far, only less than 100 cases have been reported.CASE DETAILS:  A 3-hour old newborn was diagnosed with aphalia after being referred from health center for respiratory distress and congenital malformation of the external genitalia. He had deranged renal function tests, hypoplastic kidneys, small patent foramen ovale and ventricular septal defect. Management of the acute conditions and parental counseling were done, but he passed away on the 8thday of life, due to the underlying diseases.CONCLUSION: A patient with aphalia needs thorough evaluation for possible associated malformations. Management is multistaged and multidisciplinary. Parental counselling should be started as early as possible, and their decision should be respected.KEYWORDS: Aphalia, neonate, malformations, gender reassignment