OBJECTIVES: Endoscopy is fundamental in different medical specialties, with increasing use. Endoscopes are expensive equipment, complex, thermo sensitive, delicate materials and submitted to high-level disinfection (HLD). The most commonly used disinfectant is glutaraldehyde (GLU) due to its high compatibility with the materials and low cost. However, evidence of toxicity to professionals and the identification of mycobacteria tolerant to GLU caused changes in Brazilian legislation on the issue, pressing health services to search for alternative desinfectants. Search for evidence on the effectiveness, toxicity and potential damage to endoscopes by alternative disinfectants to GLU available in the Brazilian market. METHODS: The study sample was semi-critical endoscopes flexible (digestive, respiratory and cystoscope), the intervention was HLD with peracetic acid (PA), Ortho-Phthalaldehyde (OP) and Electrolyzed Acid Water (EAW), compared to GLU, with outcomes HLD effectiveness, toxicity and damage to equipment. RESULTS: Were identified 822 publications (2008-2013) on 13 databases, 23 studies were selected considering the best quality of available evidence. As for effectiveness, the findings draw attention to the intrinsic resistance of subclass Coccidia spp to all evaluated disinfectants and acquired tolerance by GLU strain of Mycobacterium massilienses which caused an outbreak of infection with more than 2000 cases in Brazil. About toxicity, the most frequently reported adverse events are colitis (no definitive causal relationship with the germicide used) and anaphylactic reactions by OP in cystoscopy. There is lack of published data on damage caused in endoscopes by the disinfectants; the few studies on the theme indicate the importance of adequate handling of equipment for conservation of its functionality. CONCLUSIONS: The publications show superiority of the PA and OP for efficacy in HLD. Only the OP clearly had adverse event related to their use. There is insufficient evidence in literature to assert the inferiority of some disinfectant for damage to equipment.