Tracheal agenesis (TA) is a rare congenital anomaly that is incompatible with prolonged life. It may occur alone or with other associated anomalies. A term infant presented with cyanosis, hypotonia, absence of crying and respiratory distress at birth. Intubation was difficult. Esophageal intubation was performed under laryngoscopy. As TA was suspected, a bronchoscopy was performed and the infant was found to have a normal epiglottis and vocal cords; however, there was no trachea. Cardiorespiratory deterioration developed and the patient died on the night of the second day at the postnatal age of 41 hours. Tracheal agenesis was confirmed at autopsy. Associated anomalies included bronchoesophageal fistula, double outlet of the right ventricle with ventricular septal defect, bicuspid pulmonary valve, single lobe of the right lung, imperforate anus and a rectourethral fistula. According to development theory, tracheal agenesis and VACTERL (vertebral defects, anal atresia, cardiovascular defects, tracheoesophageal fistula, radial dysplasia or renal defects and limb defects association may result from a mesodermal deficiency caused by abnormal blastogenesis.