In this report we describe a newborn with a rare case of Type II tracheal agenesis and bronchoesophageal fistula. Polyhydramnios and suspected esophageal atresia were identified during routine pre-natal ultrasound screening. Upon delivery, rigid bronchoscopy, esophagoscopy, and intraoperative fluoroscopy were performed, where both bronchi and the carina showed unusual horizontal orientation making it difficult to identify the fistula. However, a post mortem CT confirmed the diagnosis of an isolated Type II tracheal agenesis with bronchoesophageal fistula.