Gastrointestinal endoscopy is gaining popularity for diagnostic and therapeutic purposes. However, concerns over endoscope-related nosocomial infections are increasing, together with interest by the general public in safe and efficient endoscopy. For this reason, reprocessing the gastrointestinal endoscope is an important step for effective performance of endoscopy. Disinfectants are essential to the endoscope reprocessing procedure. Before selecting an appropriate disinfectant, their characteristics, limitations and means of use must be fully understood. Herein, we review the characteristics of several currently available disinfectants, including their uses, potency, advantages, and disadvantages. Most disinfectants can be used to reprocess gastrointestinal endoscopes if the manufacturer's guidelines are followed. The selection and use of a suitable disinfectant depends on the individual circumstances of each endoscopy suite.