Bronchoscopy is a procedure that provides direct visualization of the tracheobronchial tree, typically to the subsegmental level. The fiberoptic bronchoscope is used in most cases, but rigid bronchoscopy is valuable in specific circumstances, including massive hemorrhage and foreign body removal. Flexible fiberoptic bronchoscopy allows visualization of the airways; identification of endobronchial abnormalities, including tumors and sites of bleeding; and collection of diagnostic specimens by washing, brushing, biopsy, or lavage. Washing involves instilling sterile saline through the bronchoscope channel onto the surface of a lesion; part of the saline is suctioned back through the bronchoscope and processed for cytology and microorganisms. Bronchial brushings can be obtained from the surface of an endobronchial lesion or from a more distal mass or infiltrate (potentially with fluoroscopic guidance) for cytologic and microbiologic studies. Biopsy forceps can be used to obtain biopsies of endobronchial lesions or passed into peribronchial alveolar tissue (often with fluoroscopic guidance) to obtain transbronchial biopsies of more distal lung tissue. Transbronchial biopsy is particularly useful in diagnosing diffuse infectious processes, lymphangitic spread of cancer, and granulomatous diseases. Complications of transbronchial biopsy include hemorrhage and pneumothorax.

Bronchoalveolar lavage (BAL) is an adjunct to fiberoptic bronchoscopy, permitting collection of cells and fluid from distal air spaces. After wedging the bronchoscope in a subsegmental airway, saline is instilled and then suctioned back through the bronchoscope for analyses, which can include cytology, microbiology, and cell counts. BAL is especially useful in the diagnosis of P. jirovecii pneumonia and some other infections.

Additional bronchoscopic approaches to obtain tissue samples from locations adjacent to the trachea or large bronchi for cytologic assessment of malignancy include transbronchial needle aspiration (TBNA). TBNA can be supplemented with endobronchial ultrasound (EBUS), which can allow guided aspiration of hilar and mediastinal lymph nodes based on real-time ultrasound images.