Concerns exist about effective methods for endoscope cleaning, disinfection and sterilization. The aim of this study was to establish a model for controlling the function of automatic washer/disinfectors for flexible endoscopes under routine conditions. The team developed a dummy endoscope channel system representing two complete gastroscopes and a colonoscope, with channels joined together and fitted with adaptors to allow the models to fit into different washer/disinfectors. The models were artificially contaminated with various combinations of four test organisms and coagulating blood and run through test cycles in different washer/disinfectors. A total of 24 test runs were performed. The reduction of a given microbial burden by at least five log steps is an established measure of efficacy of a decontamination procedure. When the two challenge tests (45 channels) and the six positive controls are excluded, only 13/309 channels (4.2%) failed the proof of efficacy. In contrast, the failure rate in the challenge test was 65.3%. The difference of the final bioburden is statistically significant. The data suggest this test model could be regarded as a first step in rational and reliable biological control of flexible endoscope reprocessing.