Most endoscopy clinics use 2% glutaraldehyde as a high-level disinfectant for reprocessing flexible endoscopes. However, even with contact times greater than 30 minutes, survival of organisms has been documented. We compared the high-level disinfection capabilities of glutaraldehyde (45-minute immersion) with a new peracetic acid germicide (20- to 25-minute immersion). Channels, valve housings, and outer sheaths were sampled to quantify bioburden levels after a patient procedure, after manual cleaning, and after disinfection. Total mean bioburden after clinical use was greater than 6 log10colony-forming units (CFU). Manual cleaning reduced the bioburden by means of 4.7 log10CFU (gastroscopes) and 6.2 log10CFU (colonoscopes). High-level disinfection with the new product was achieved in five of six (product stressed by EPA Reuse Test) and 7 of 10 (product stressed by dilution and organic load) successfully disinfected endoscopes, whereas glutaraldehyde achieved it in 4 of 10 (product stressed by dilution and organic load). We conclude that the new peracetic acid product (20- to 25-minute contact time) is at least as effective as glutaraldehyde (45-minute contact time) for reducing the bioburden of vegetative aerobic organisms in endoscopes.