We reported a case of tracheal agenesis (TA) that was diagnosed during surgery. A female infant, weighing 1,104 g, was born at the 29 weeks of gestation. She showed severe respiratory distress without crying. Oxygenation was improved by mask ventilation, but tracheal intubation was very difficult. Tracheoesophageal fistula (TEF) was suspected because significant amount of air from nasogastric tube was noticed. Physical examination and X-ray findings suggested Gross E type TEF, duodenal atresia and cloaca. On the second day of life, ligation of TEE gastrostomy and colostomy were scheduled. Although operation was started without problems, ventilation became impossible when TEF was clamped and release of clamping made it possible. Bronchoscopic investigation revealed that tracheal tube was located in the esophagus. We have never doubted the esophageal intubation, because patient was ventilated preoperatively and signs of respiratory distress syndrome were successfully treated by the surfactant replacement therapy through tracheal tube. Type II TA according to Floyd's classification was diagnosed by bronchoscopic and echographic investigations. Distal esophageal ligation, gastrostomy and esophagostomy were performed. She died on the 12th day of life in spite of vigorous ventilatory and cardiovascular support.