Objective To investigate the current status of cleaning and disinfection of endoscopic biopsy valves in three digestive endoscopy centers in Jiangxi Province, and evaluate the effectiveness of establishing a standard operational procedure (SOP) of cleaning and disinfection for flexible endoscopic biopsy valves. Methods The cleaning and disinfection procedures of biopsy valves in three digestive endoscopy centers were recorded using on-site investigation method (the control group). Based on relevant literature and manufacturer manuals at home and abroad, SOP was established and cleaning and disinfection training for cleaning professional was provided (the trial group). Biopsy valve specimens from two groups were taken. The disinfection qualified rate, microbial positivity rate before disinfection, and microbial load after disinfection before and after procedure improvement were compared between two groups. Results A total of 180 biopsy valve specimens were taken from two groups (60 specimens from endoscopy centers A, B, and C each). On-site investigation showed that the cleaning and disinfection procedure for biopsy valves was inconsistent among the three endoscopy centers. The total qualified rate of disinfection in the trial group was higher than that in the control group (95.5% vs 83.3%), with statistically significant difference (P<0.05). The total microbe positive rate of biopsy valves from the trial group was lower than that from the control group (25.0% vs 57.2%), with statistically significant difference (P<0.05). The difference in microbial load after disinfection between two groups of biopsy valves was statistically significant (Z=-6.47, P<0.05). Conclusion Although being a tiny accessory, the flexible endoscopic biopsy valve can be a potential source of infection if not tho-roughly cleaned and disinfected. Developing SOP can help improve the cleaning effectiveness of biopsy valves. At present, there is no unified standards for the cleaning and disinfection procedure of endoscopic biopsy valves. In the future, standardization of the SOP for biopsy valves should be continuously explored, so as to reduce the risk of cross infection.