Spread of infection through the flexible bronchoscope is underrecognized and underreported. Prevention of bronchoscopy-induced infection requires increased vigilance by the physician, assiduous implementation of reprocessing protocols, and closer collaboration between bronchoscopy personnel, infection control practitioners, and instrument manufacturers. Patient safety depends on adequate disinfection of bronchoscopes and accessories used, as well as proper training of bronchoscopists, nurses, and ancillary staff. It is important to recognize that microbial transmission may occur via any part of instruments or anything in contact with the instruments including cleaning solutions, automated washers, and rinsing water. Numerous surveys have suggested poor adherence to published preventive guidelines. To address the challenges of reprocessing bronchoscopes, all users must comply with guidelines for cleaning and disinfection and each procedure should be performed with a clean, disinfected bronchoscope.