We report on a neonatal case of thoracoabdominal duplication associated with a split notochord syndrome and multiple anomalies. A newborn girl had severe dyspnea and was transferred to our neonatal care unit. At laparotomy, the entire small bowel was herniated into the posterior mediastinum through a defect in the right hemidiaphragm. The small bowel mesentery was firmly fixed to the mediastinum such that a large part of the small bowel could not be repositioned into the abdominal cavity. Imaging studies revealed an absent inferior vena cava with an azygous continuation. The superior mesenteric vein joined the splenic vein to form a portoazygous shunt that ran caudally through the mediastinum and drained into the azygous vein. The patient's intrahepatic portal vein was completely absent. To the best of our knowledge, this is the first reported case of a thoracoabdominal duplication associated with a portoazygous shunt. The etiopathogenesis and surgical management of this complicated case are discussed.