Aphallia (absence of penis) is an extremely rare abnormality which has rarely been described in medical literature and can be part of the urorectal septum malformation sequence (URSMS). URSMS has hardly been reported in medical literature and includes the absence of perineal and anal openings in association with ambiguous genitalia and urogenital, colonic, and lumbosacral anomalies. This case report tells the importance of detailed examination of infants that are diagnosed with aphallia. We report a case of a newborn who was diagnosed as aphallia with the URSMS syndrome after birth. The neonate had an endocardial cushion defect (atrial septal defect and ventricular septal defect) and bilateral agenesis of the kidney. The neonate succumbed to death secondary to hypoplastic lung leading to respiratory failure.