Transmission of infection related to gastrointestinal endoscopy continues to be a subject of much discussion. The principles of infection control during endoscopy are reviewed. Guidelines set forth by a number of gastrointestinal endoscopy associations have emphasized the need for meticulous cleaning of endoscopes immediately after use, followed by appropriate disinfection, rinsing and drying. Most, if not all, episodes of transmission of infection during endoscopy are associated with lapses in cleaning and disinfection protocols. The need for universal compliance with infection control standards, and for the development of strategies to achieve such compliance, is highlighted.