The clinical and radiographic presentation of pulmonary disease in organ-transplant recipients often fails to allow the specific identification of a causative pathogen or permit the distinction between infectious and noninfectious processes. Frequently, invasive procedures are required to make a specific diagnosis and initiate appropriate therapy. The early use of transtracheal aspiration proved useful for the diagnosis of bacterial and mycobacterial pneumonias. However, its inability to reliably prove pneumonia caused by opportunistic pathogens, such as Pneumocystis carinii and cytomegalovirus, led to very narrow indications for its use among organ-transplant recipients. The introduction of fiberoptic bronchoscopy in the 1970s, with its large variety of related procedures, revolutionized the approach to the diagnosis of pulmonary disease among immunosuppressed patients and today remains the initial procedure of choice in the majority of clinical situations. The diagnostic success and relatively low morbidity of bronchoscopy has narrowed the indications for surgical lung biopsy, despite its excellent diagnostic yield. Open or thoracoscopic lung biopsies are most often used where bronchoscopy has failed to make a diagnosis or where the risk of bleeding prohibits a bronchoscopic biopsy.