The advantages of diagnostic and therapeutic endoscopy are considerable, as are the problems associated with decontamination. The relatively high cost of these instruments and an escalation in the demand for endoscopy have resulted in there being too few instruments to provide one for each patient on a list. Consequently little time is available for decontamination between patients. Despite this, the incidence of post-procedural infection appears to be low. This is presumably because either the infection risk is indeed low or patients were observed only for a short time and no associations were made between subsequent infection and the endoscopic procedure. The greatest problem with processing lies with heat-sensitive instruments, which are usually disinfected by immersion in glutaraldehyde. Aldehydes are irritant and sensitizing and therefore stringent precautions have to be taken to avoid inhalation, skin and eye contact. Thorough rinsing and automated processing are advised but this procedure has, on occasions, led to infection and pseudo-infection.