Abstract: OBJECTIVE To conduct the microbiological monitoring of final rinse water for flexible endoscopes in 30 tertiary medical institutions in Shanghai and investigate the current situation of disinfection of water pipes. METHODS In situ sampling of the final rinse water for the flexible endoscopes was carried out in the hospitals, the membrane filtration method was applied for culture and identification, meanwhile, the questionnaire survey on disinfection of water pipelines was also conducted. RESULTS A total of 84 final rinse water samples were collected, and the overall qualified rate was 63.09%. The median bacterial colony counts of the unqualified water samples was 72 (35-236). The qualified rate of the final rinse water samples that were taken from the water pipelines used for less than 1 year was the highest, and the qualified rate of the final rinse water samples that were taken from the water pipelines used for more than 5 years was the lowest. CONCLUSION The qualified rate of the final rinse water for flexible endoscopes is high in the tertiary medical institutions in Shanghai, the service life of the water pipe is a major influencing factor. It is necessary for the medical institutions to rigidly follow the rules and strengthen the monitoring of the final rinse water.