Background: This study was conducted in order to survey the current state of cleaning, disinfection, rinsing, drying, and storage of gastrointestinal endoscopes. Methods: Eighty hospitals were selected through convenient sampling. Self-reported questionnaire was distributed from September 14 to October 10 in 2015. Results: The response rate was 67.5% (54/80). In 88.9% of the hospitals, reprocessing was performed in a cleaning space separated from the laboratory and 88.9% used an enzymatic cleaner. Disinfectants used were ortho-phthalaldehyde in 63.0%, and paracetic acid in 33.3%. Eighty seven percent of the hospitals used test strips in order to test the effective concentration of disinfectant and in 61.1%, drying was done through passing air and over 70% alcohol. Microbial culture for the quality control of gastrointestinal endoscopes was performed in 77.8%. In the comparison of the adequacy of gastrointestinal endoscope reprocessing, it was observed that gastrointestinal endoscopes were reprocessed more adequately in larger and tertiary care hospitals. Conclusion: Gastrointestinal endoscopes were reprocessed in similar manners, but there were differences in the detailed process. It is still necessary to segment reprocessing into stages, to prepare standardized guidelines, and to monitor compliance with the guidelines.