Recurrent episodes of endoscope contamination with nontuberculous mycobacterium and Pseudomonas species, coupled with employee concerns about exposure to 2% glutaraldehyde and the requirement for rapid scope turnover time, led to the investigation of an alternative method for endoscope processing. A prospective evaluation of 220 bronchoscopy procedures was carried out. Endoscope culture surveillance was performed twice a month for a 12 month period on all endoscopes. In addition, the deliberate inoculation of bronchoscopes with Mycobacterium gordonae was carried out. No indications of cross contamination were noted among the 220 bronchoscopy procedures after processing the scopes by the studied liquid chemical sterilization system using peracetic acid. Ongoing patient surveillance did not reveal any indications of cross contamination for nearly 15,000 patients diagnostic or surgical endoscopic procedures using instruments processed by this liquid chemical sterilization system. Twice a month for 12 months, bronchoscopes, colonoscopes, and gastroscopes were cultured for bacterium, fungi, and acid fast bacilli and showed no growth. Deliberate inoculation of bronchoscopes with M. gordonae showed the scopes were rendered sterile. No unusual occurrences of occupational chemical exposure were found in 11 individuals working with this liquid chemical sterilization system. The peracetic acid based sterilization system studied proved to be an effective, safe, and economical alternative to the glutaraldehyde method.