Technologic advances in the last 30 years have resulted in the development of complex, expensive, and heat sensitive medical instrumentation, including flexible gastrointestinal endoscopes. Because of the design complexity and the region of use, gastrointestinal endoscopes present special challenges to cleaning. If instruments are not properly cleaned the disinfection or sterilization procedure can fail and increase the possibility of infection transmission from one patient to another. Although the cleaning process removes intestinal microflora, the washing process itself may introduce a saprophytic or environmental microbial flora. It has been repeatedly shown that endoscope cleaning, not the disinfection or sterilization procedure, controls the success of the reprocessing procedure.