Flexible endoscopes are complex, delicate and expensive reusable instruments that require specialist decontamination to prevent transmission of patient infection and to preserve the instruments in optimal working order. As they are damaged by heat, they cannot be steam sterilised as would be used for most equivalent surgical instruments. Instead, they need careful cleaning and disinfection with compatible chemicals, followed by drying and careful storage. Most endoscopes have a variety of internal, narrow lumens running the length of the instrument; cleaning and disinfection of these is probably the most challenging element of reprocessing. The stages in typical endoscope reprocessing are 1) manual cleaning immediately after use to remove gross soiling, 2) subsequent manual cleaning to a higher standard to remove the majority of remaining soil and 3) reprocessing in an endoscope washer-disinfector to finish the cleaning, chemically disinfect the instruments, rinse with low contamination water and dry the endoscopes. The endoscopes can then be used within a short time period or, if longer storage is required, can be kept in cabinets that will irrigate them, internally and externally, with filtered air. The facility where endoscopes are reprocessed should facilitate the monitored movement of individual endoscopes from dirty (as received) through the individual steps of decontamination in a validated process until safe for reuse. This process should minimise the risk of recontamination and ensure that endoscopes that have not yet been fully decontaminated cannot be issued for use.