Thoracic congenital malformations may be associated with long-term pulmonary morbidity. Certainly, this is the case for Esophageal Atresia (EA) and Congenital Diaphragmatic Hernia (CDH). These conditions have variable degrees of impaired development of both the airways and the lung vasculature, with a postnatal impact on lung function and bronchial reactivity. Pulmonary complications themselves are frequently associated to non-pulmonary morbidities, including gastrointestinal and orthopaedic complications. These are best recognized in a structured multidisciplinary follow-up clinic and can be actively and precociously managed in order to provide adequate support and improve the quality of life of the patients.