Background: Diseases of the lungs and airways can be life-threatening in patients with congenital cardiac disease. External compression, and tracheobronchomalacia, as well as pathology of the large airways, can cause respiratory symptoms such as wheezing, stridor, fever, and dyspnoea, along with producing difficulty to wean the patient from mechanical ventilation. A definite diagnosis may be achieved by fibreoptic flexible bronchoscopy. Aims: To characterize the patients who underwent bronchoscopy for respiratory diseases associated with congenital cardiac disease, and to evaluate the safety, total diagnostic rate, and diagnostic rate, which yielded alteration of treatment in this group of patients. Methods: We reviewed retrospectively the records of 39 patients with congenital cardiac disease associated with abnormalities of the airways who underwent 49 fibreoptic bronchoscopies between 1999 and 2004. The patients were evaluated with regard to rate of diagnosis, the rate of procedures that resulted in alteration of management, and the rate of complications. Results: Fibreoptic flexible bronchoscopy was safe, and contributed to a specific diagnosis in almost nine-tenths of the procedures. A specific diagnosis that resulted in treatment alteration was achieved in one-fifth of the procedures. Conclusions: Fibreoptic flexible bronchoscopy has an important role in the evaluation of pulmonary abnormalities in patients with congenital cardiac diseases, and should be considered as an initial diagnostic tool that may guide the clinician with regard to the proper therapy.