The technique of flexible bronchoscopy creates unique research opportunities to investigate the underlying mechanisms of respiratory disease in children, by sampling directly from the airway. Bronchoscopy is, however, invasive and the ethics of performing this type of procedure for research purposes must be considered carefully at the outset. This article discusses the research applications of bronchoscopy in children, focusing on the ethical and safety issues, the types of procedure that can be performed and their application to the investigation of specific diseases. Acceptance of the use of bronchoscopy as a research tool is increasing. Future work should focus on the comparison of invasive and non-invasive techniques, the use of bronchoscopy in longitudinal and interventional studies and the development of new, highly sensitive techniques to allow us to study disease pathogenesis in greater detail. Collaboration between centres should be encouraged to maximise the use of samples obtained.