Gastrointestinal endoscopy can lead to infectious complications, and endoscopes must be disinfected to prevent them. OBJECTIVE to evaluate three methods of disinfection: 1) usual cleaning technique and immersion in glutaraldehyde phenolate (GP); 2) meticulous cleaning and immersion in GP, and 3) meticulous cleaning and immersion in hydrogen peroxide. METHODS thirty endoscopes (15 gastroscopes and 15 colonoscopes) were disinfected with each method. Samples were taken following endoscopic exploration, after cleaning and after disinfection, and were cultured. The number of positive culture (cfu/ml > 1) was counted. RESULTS the rate of contamination of endoscopes did not decrease significantly after cleaning with method 1 (66 vs 60%), but did decrease with method 2 (38 vs 16%) and method 3 (53 vs 17%). The contamination rate after cleaning was significantly lower with methods 2 and 3 (p < 0.005). This rate was also lower after disinfection (p < 0.025). Method 3 achieved 0% contamination following disinfection. CONCLUSIONS the greatest decrease in contamination rate was achieved with conscientious cleaning followed by disinfection. Both disinfectants yielded similar results, although hydrogen peroxide produced a higher level of disinfection.