BACKGROUND Public concern has been raised with regard to the possibility of transmission of instrument mediated Helicobacter pylori infection after upper gastrointestinal endoscopy. METHODS Disinfection procedures for gastrointestinal endoscopes were surveyed in 20 Japanese institutions, and in vitro bactericidal activities of seven disinfectants against H. pylori were determined. RESULTS Screening tests for infection before endoscopy were not consistently performed; only 11 institutions always screened for hepatitis B virus, nine for hepatitis C virus, and two for tuberculosis. All 20 institutions used the same flexible fiberoptic endoscope on more than one patient in succession, with minimal cleanings only. Only two used glutaraldehyde for disinfection. Most used ethyl alcohol, benzalkonium chloride, or alkyldiaminoethylglycine hydrochloride as an external wipe. Bactericidal testing of nine strains of H. pylori against disinfectants revealed that ethyl alcohol (80%) and glutaraldehyde (0.5%) killed all nine strains within 15 seconds, whereas chlorhexidine gluconate (0.05%, 0.1%), benzalkonium chloride (0.025%, 0.1%), alkyldiaminoethylglycine hydrochloride (0.1%), povidone-iodine (0.1%), and sodium hypochlorite (150 ppm) killed all nine strains within 30 seconds. CONCLUSIONS H. pylori is readily killed by many common disinfectants and antiseptics. However, practices for disinfection of flexible fiberoptic endoscope were not appropriate.