Background/Aims: Safety of endoscopic procedures has been a major issue over the last 10 years. Most endoscopy units use 2% glutaraldehyde and automated endoscope reprocessors (AERs) for disinfecting gastrointestinal endoscopes. We attempted an in-use evaluation of the current reprocessing procedures. Methods: Thirty flexible endoscopes were randomly collected just after upper endoscopic examinations and were disinfected using 2% glutaraldehyde in an AER. Cultures were taken from biopsy channels (S-l), tip of the insertion tubes (S-2), umbilical cords (S-3), and angulation knobs (S-4). Results: In 63,3% (19/30) of endoscopes, there was no microbial contamination after disinfection procedures. The culture positive rates of S-l, S-2, S-3, and S-4 samples were 20,0%, 0.0%, 3.3%, and 20.0%, respectively. Microorganisms of 13 species were identified, but there was no pathogen related with reported infectious complications after endoscopic procedures. Conclusions: Current disinfection procedure using 2% glutaraldehyde and an AER appears to be very effective in decontaminating patient-used endoscopes. Low level microbial contamination of endoscopes after conventional reprocessing methods may not impose great risk on patients. (Korean J Gastrointest Endosc 2001;22:393-398)