ObjectiveTo evaluate membrane filtration (MF) method and agar plate pouring (AP) method for detecting endoscopy disinfection efficacy. MethodsDisinfection efficacy of all endoscopes in a hospital were detected and evaluated with MF method and AP method. ResultsA total of 192 disinfected endoscopes were detected, 96 were detected with MF method and 96 were detected with AP method, according to the detected bacterial colony count, disinfected endoscopes were divided into 0, 1-10, 11-20, 21-300, and > 300 CFU/piece groups, ranksum test results showed differences in distribution of colony count of disinfected nasopharyngoscopes, bronchoscopes, gastroscopes, and enteroscopes were significant(all P<0.05), bacterial colony count detected by MF method was higher than AP method. Qualified rate of endoscope disinfection detected by AP method was 91.67%, MF method was 88.54%, there was no significant difference in qualified rate between two methods (χ2=0.53, P=0.630). ConclusionMF method is more accurate than AP method to detect bacterial colony count remained in the endoscope after disinfection, it is worth to be popularized.