Objective To compare the effect of automatic cleaning and disinfection machine as well as traditional manual cleaning and disinfection method on the cleaning and disinfection of digestive endoscopes. Methods 109 digestive endoscopes in a digestive endoscopy center of a hospital were collected and divided into trial group and control group according to their numbers, trial group was cleaned and disinfected by automatic cleaning and disinfection machine, control group was cleaned and disinfected by traditional manual cleaning and disinfection method. Samples were taken from different parts of endoscopes in two groups. Cleaning quality of endoscopes was detected by visual method and ATP biofluorescence detection method, and bacterial contamination of endoscopes was detected by poured-plate culture method. Qualified rate of cleaning and disinfection of endoscopes between two groups was compared. Results There were 55 endoscopes in trial group and 54 in control group. The total qualified rates of endoscope cleaning in trial group and control group were 94.55% and 83.33% respectively, there was no significant difference between two groups (P>0.05). Qualified rate of endoscopic valve cleaning in trial group was higher than control group (96.36% vs 85.19%, P<0.05), but there was no significant difference in qualified rates of endoscopic surface cleaning and endoscopic lumen cleaning between two groups(both P>0.05). The total qualified rates of endoscope disinfection in trial group and control group were 96.36% and 85.19% respectively, there was significant difference between two groups (P<0.05). Qualified rate of endoscopic lumen disinfection in trial group was higher than control group (96.36% vs 85.19%, P<0.05), but there was no significant difference in the qualified rates of endoscopic surface and valve between two groups (both P>0.05). Conclusion Effect of automatic cleaning and disinfection machine on cleaning and disinfection of digestive endoscopes is superior to traditional manual clea-ning and disinfection. If traditional manual cleaning and disinfection of endoscopes is adopted, cleaning and disinfection criteria of soft endoscopes should be strictly enforced to minimize the risk of cross-infection during endoscopy diagnosis and treatment.