BACKGROUND Respiratory complications are common after neonatal repair of oesophageal atresia and tracheo-oesophageal fistula. The prevalence of lung function abnormalities and the relation between gastrointestinal complications and lung function has not been studied in a large number of patients. METHODS Lung volumes and flow-volume loops were measured in 155 patients without spinal curvature aged 6-37 years who had undergone surgery for oesophageal atresia and tracheo-oesophageal fistula. RESULTS Sixty four of the 155 patients had evidence of mild lower airways disease, with values for FEV1 more than two standardised scores below the predicted value in 39 (25%) and above 2 standardised scores for the residual volume (RV)/total lung capacity (TLC) ratio in 64 (41%). Restrictive lung disease (TLC more than 2 standardised scores below predicted) was present in 28 (18%). Severe lung function abnormalities were present in under 10% of the 155. Half the subjects had some evidence of extra-thoracic tracheal obstruction, with a high ratio of expiratory to inspiratory flow for peak flow in 76 (50%) and at 50% of vital capacity in 59 (38%). Patients with radiological gastro-oesophageal reflux in early childhood had more airways obstruction and smaller lung volumes. Patients with current gastrointestinal symptoms were similar in their lung function to symptom free patients. CONCLUSIONS Minor lung function abnormalities are common in patients after repair of oesophageal atresia. Early diagnosis and management of gastro-oesophageal reflux may help to minimise these lung function abnormalities.