Thorough cleaning and disinfection or sterilization of endoscopes and associated equipment will reduce the likelihood of misdiagnosis and post-procedural infection. It will also prevent instrument deterioration and malfunction. With a rapid escalation in demand for endoscopy, particularly that associated with minimally invasive surgery, it is important that we have the processing technology to match the diagnostic and therapeutic value of these instruments without exposing staff and patients to unnecessary risk. Wherever possible staff should purchase heat tolerant endoscopic equipment that is readily accessible for cleaning. Automated processors, e.g. washer disinfectors and ultrasonic cleaners, improve the quality of the decontamination process but machines must have a self-disinfect function to prevent instrument recontamination during processing. Sterile, or filtered bacteria-free, water is essential for bronchoscopes and invasive instruments. Glutaraldehyde is still the most widely used disinfectant, particularly for the heat sensitive flexible endoscopes, but it is irritant and sensitizing and a safer alternative is sought. Peracetic acid is more rapidly efficacious and probably less irritant and, provided it does not damage endoscopes and processing equipment, may prove a suitable alternative. Unfortunately there are no nationally agreed test methods for assessing this and other new endoscope disinfectants and therefore no register of suitable or approved products. There is also no proven safe alternative to ethylene oxide for sterilizing invasive heat labile flexible endoscopes. It is important that, if toxic disinfectants and sterilants are used, staff and patients are suitably protected from exposure. Update training is essential for all processing staff if infection risks are to be minimized and sensitization problems avoided.