Abstract: Objective To compare tryptone glucose extract agar (TGEA) method with nutrient agar medium method in the monitoring of final rinse water, comparing reagent kit membrane filtration method with traditional membrane filtration method in the quality monitoring of endoscope disinfection. Methods The basic information of endoscope center was investing from 24 hospitals in Tianjin. The way of random sampling was used to sample the final rinse water and the flushing water of the endoscope biopsy channel. Using two methods respectively to detect the number of bacterial colonies. Results Compared with nutrient agar medium method, TGEA method has the statistical significant (P < 0.05) higher detection rate (96.7% vs 73.3%) and bacterial colony number (median 44 CFU/100 ml vs 8 CFU/100 ml) when monitoring final rinse water. Bland-Altman analysis shows that these two methods are lack of consistency. On the contrary, when monitoring endoscopic disinfection effect, these two methods show similar results (P > 0.05) in both detection rate (60.0% vs 56.7%) and bacterial colony number (median 2 CFU/piece vs 1 CFU/ piece). And the consistency can be proved by Bland-Altman analysis. Conclusions According to the survey analysis, there are still plenty of rooms for the improvement of monitoring level and the standardization of test method when dealing with final rinse water and endoscopic disinfection effect. TGEA method is proved to be more sensitive and clinically adaptable for the detection of final rinse water, while reagent kit membrane filtration method has its strengths in portability, efficiency, accuracy and operation simplicity. Both two methods would be suitable for the routine monitoring of endoscope center in hospitals.