Total aganglionosis of the colon presenting with small intestinal obstruction in the neonatal period was observed in combination with congenital alveolar hypoventilation requiring continuous mechanical ventilation in a boy. The patient died aged 15 months from acute dehydration due to enteritis, long after total resection of the aganglionic bowel had been performed. Pulmonary hypertension was found in the newborn period. There was progressive right ventricular myocardial hypertrophy. This is the fourth case reported with a combination of defects involving nerve cell function of the brain stem and gastrointestinal tract.