Laryngeal atresia (LA) is an uncommon congenital anomaly, and only a few cases with long-term survival are reported in the literature. The authors describe a 2-year-old boy with LA and esophageal (EA), intestinal, and urethral atresia (UA). Immediately after birth, severe respiratory distress and mild abdominal distension became evident. Endotracheal intubation was unsuccessful and emergency tracheal puncture was performed, after which a tracheostomy was constructed. Direct laryngoscopy revealed LA at the vocal cord level. A cystostomy and gastrostomy were constructed immediately because of UA and EA. A cystocutaneostomy, ileocolic anastomosis, and resection of a tracheoesophageal fistula (TEF) were simultaneously performed 1 day after birth. The EA was proximal with a distal TEF. The gap between the ends of the upper and lower esophagus was 4 cm in length. It was thought impossible to perform a primary anastomosis, and therefore, a gastrostomy and resection of the TEF using multiple-stage surgery was undertaken. Intestinal resection and anastomosis were performed due to intestinal stenosis from necrotizing enterocolitis at the age of 3 months. Hypoxic encephalopathy developed due to accidental obstruction of the tracheostomy tube at the age of 10 months, and physical therapy was begun. He required a cutaneous nephrostomy due to a right hydromegaureter with vesicoureteric reflux and a left non-functioning kidney at the age of 23 months. He has been hospitalized for partial ventilatory assistance for 2 years at our institution. The course of this patient seems noteworthy in relation to the genesis of the multiple malformations.