To review reports on the transmission of infections by flexible gastrointestinal endoscopy and bronchoscopy in order to determine common infecting microorganisms, circumstances of transmission, and methods of risk reduction. Relevant English-language articles were identified through prominent review articles and a MEDLINE search (1966 to July 1992); additional references were selected from the bibliographies of identified articles. All selected articles related to transmission of infection by gastrointestinal endoscopy or bronchoscopy; 265 articles were reviewed in detail. Two hundred and eighty-one infections were transmitted by gastrointestinal endoscopy, and 96 were transmitted by gastrointestinal endoscopy, spectrum of these infections ranged from asymptomatic colonization to death. Salmonella species and Pseudomonas aeruginosa were repeatedly identified as the causative agents of infections transmitted by gastrointestinal endoscopy, and Mycobacterium tuberculosis, atypical mycobacteria, and P. aeruginosa were the most common causes of infections transmitted by bronchoscopy. One case of hepatitis B virus transmission via gastrointestinal endoscopy was documented. Major reasons for transmission were improper cleaning and disinfection procedures; the contamination of endoscopes by automatic washers; and an inability to decontaminate endoscopes, despite the use of standard disinfection techniques, because of their complex channel and valve systems. The most common agents of infection transmitted by endoscopy are Salmonella, Pseudomonas, and Mycobacterium species. To prevent endoscopic transmission of infections, recommended disinfection guidelines must be followed, the effectiveness of automatic washers must be carefully monitored, and improvements in endoscope design are needed to facilitate effective cleaning and disinfection.