Tracheomalacia is an abnormality of the trachea that probably is present to some degree in all infants and children with oesophageal atresia. It causes the trachea to collapse during breathing, leading to obstruction of the upper airway. Our knowledge of the structural abnormalities underlying tracheomalacia is limited, mainly because patients with oesophageal atresia usually survive. Recently, the Adriamycin-induced rat model of oesophageal atresia and tracheomalacia has clarified some aspects of its pathology and the factors which may influence its development. The rat model suggests that the same detrimental factors that cause oesophageal atresia might also affect the development of the trachea, and that anomalous great vessels may exacerbate the severity of tracheomalacia locally.