A common upper airway and digestive tract is a rare congenital anomaly that is usually fatal and its exact incidence is not known. It is a diagnostic challenge as it requires high index of suspicion. It should be considered in a neonate with respiratory distress in a non-vigorous baby requiring endotracheal intubation, which is difficult even in expert hand. We present a newborn with suspected tracheo-esophageal fistula that was diagnosed intraoperatively to have absent upper blind pouch of the esophagus and on autopsy found to have laryngeal atresia with absent vocal cords and a common aerodigestive tract continuing distally with trachea. The neonate was ventilated with endotracheal tube (ETT) placement which in retrospect we came to know that it was in the esophagus. The neonate also had associated multiple congenital anomalies of VACTERL association. The importance of teamwork between neonatologist, pediatric surgeon, anesthesiologist, and radiologist is highlighted for diagnosis and management of such rare cases.