As infection-related issues have become one of the most important concerns in endoscopy centers, proper reprocessing of endoscopes has attracted great interest. Compliance with established guidelines for reprocessing is critical to prevent pathogen transmission. However, hospital compliance with guidelines has not been satisfactory. To increase compliance, efforts have focused on developing new and more innovative disinfectants and an automated endoscope reprocessor. Reprocessing must be performed by appropriately trained personnel and regular monitoring of reprocessing is essential for quality assurance to improve compliance.