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Following surgical correction in the neonatal period, patients born with oesophageal atresia have significant co-morbidity, particularly in childhood. This study evaluates health-related quality of life and its determinants such as concomitant anomalies and the presence of respiratory and/or gastro-intestinal symptoms 6–18 years after repair of oesophageal atresia.Parents of 24 patients with oesophageal atresia completed the child health questionnaire for parents and 37 patients completed the child form. Gastro-intestinal symptoms were assessed by a validated standardized reflux questionnaire. Results were compared with a healthy reference population.Parents as well as patients themselves scored significantly lower on the domain general health perception. According to parents, general health perception was negatively affected by age at follow-up and concomitant anomalies. Patients reported that reflux symptoms reduced general health perception.In this first study describing health-related quality of life in children and adolescents born with oesophageal atresia, we demonstrated that general health remains impaired because of a high incidence of concomitant anomalies and gastrointestinal symptoms in patients with oesophageal atresia when compared with the healthy reference population.