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Objectives: To determine the efficacy of the cleaning and disinfection processes of endoscopes in a level III hospital, and to determine the most common pathogens found before and after these procedures. Methods: Case series from August to October 2010. A total of 50 cycles of cleaning-disinfection procedures were evaluated. Culture media (Brilliant blue agar, xylose-lisine-deoxycholate, sulfite bismute, Me Conkey) as well as coagulase and oxidase tests were used. Results: The mean count of bacteria before the procedures was 835.3 ± 1,114.6 UFC/ml; the median count was 233 UFC/ml; respective values after the procedures were 236.3 ± 700.7 UFC/ml and 10 UFC/ ml, respectively, a statistical difference was found (p=0.000001). Bacterial load was positive before the procedures in 88%, and 26% after them. A statistical significant difference was found for Pseudomonas aeruginosa (p = 0.006) and Salmonella entérica (p=0.00001). Bacterial load was positive in 55% after 10 days of using the disinfectant and it was 19% after the ninth day. Conclusions: The cleaning-disinfection process is not effective. Salmonella entérica, Pseudomonas aeruginosa and Escherichia coli were the most frequent isolated pathogens. The high level disinfectant (2% glutaraldehyde) is not effective after the tenth day. [ABSTRACT FROM AUTHOR]