The bioburden (blood, protein, pathogens and biofilm) on flexible endoscopes after use is often high and its removal is essential to allow effective disinfection, especially in the case of peracetic acid-based disinfectants, which are easily inactivated by organic material. Cleaning processes using conventional cleaners remove a variable but often sufficient amount of the bioburden. Some formulations based on peracetic acid are recommended by manufacturers for the cleaning step. We performed a systematic literature search and reviewed the available evidence to clarify the suitability of peracetic acid-based formulations for cleaning flexible endoscopes. A total of 243 studies were evaluated. No studies have yet demonstrated that peracetic acidbased cleaners are as effective as conventional cleaners. Some peracetic acid-based formulations have demonstrated some biofilm-cleaning effects and no biofilmfixation potential, while others have a limited cleaning effect and a clear biofilm-fixation potential. All published data demonstrated a limited blood cleaning effect and a substantial blood and nerve tissue fixation potential of peracetic acid. No evidence-based guidelines on reprocessing flexible endoscopes currently recommend using cleaners containing peracetic acid, but some guidelines clearly recommend not using them because of their fixation potential. Evidence from some outbreaks, especially those involving highly multidrug-resistant gram-negative pathogens, indicated that disinfection using peracetic acid may be insufficient if the preceding cleaning step is not performed adequately. Based on this review we conclude that peracetic acid-based formulations should not be used for cleaning flexible endoscopes. Key words: Peracetic acid; Cleaning; Flexible endoscope; Biofilm; Resistance; Bioburden; Blood; Disinfection; Reprocessing Core tip: Some formulations based on peracetic acid (PAA) are recommended by manufacturers for cleaning flexible endoscopes. We reviewed 243 studies to analyse the evidence for this recommendation. No study demonstrated that PAA-based cleaners were as effective as conventional cleaners, and some PAA-based formulations had clear biofilm-fixation potential. Dried blood and nerve tissue were substantially fixed by PAA. Some outbreaks, especially of highly multidrug-resistant gram-negative pathogens, indicated that insufficient cleaning could not be compensated for by using PAA in the disinfection step. PAA-based formulations should not be used for cleaning flexible endoscopes.