Flexible bronchoscopy with bronchoalveolar lavage and transbronchial biopsy has contributed significantly to the success of lung transplantation to detect rejection and infections (bacterial, fungal, viral, and protozoal). It permits the visualization of the airway anastomosis and also allows for the management of airway complications using interventional bronchoscopic techniques such as balloon dilatation, stent insertion, and laser. A new classification (TEGLA [thickness, extent of injury, granulation tissue, loose sutures, anastomotic complications]) for uniform reporting of airway ischemic injury is proposed. The common complications during flexible bronchoscopy include acute hypoxemia, bleeding, and pneumothorax. The management of these complications during flexible bronchoscopy and the value of surveillance and follow-up transbronchial biopsy and bronchoalveolar lavage is discussed. Bronchoalveolar lavage and transbronchial biopsy are also used for research purposes and might hopefully allow recognition of bronchiolitis obliterans at an earlier stage.