Instrument disinfectants can be based on different types of biocidal active substances such as benzalkonium chloride, DDAC, glutaraldehyde, hydrogen peroxide, peracetic acid and sodium hypochlorite. Validated reprocessing of non-critical and semi-critical medical devices is expected to provide a health benefit to patients. A low adaptive response combined with a frequently observed inhibition of biofilm formation and removal of existing biofilm cannot be attributed to any of the biocidal active substances. Overall, the use of peracetic acid on surfaces of instruments where biofilm formation is to be inhibited (e.g. flexible endoscopes) seems to be the most appropriate option due to the low selection pressure, mainly inhibition of biofilm formation and mainly moderate removal of biofilm. Hydrogen peroxide and sodium hypochlorite also have a low selection pressure and can moderately remove biofilm, but they could also increase biofilm formation in a relevant number of species. They appear to be suitable for use on instrument surfaces where the enhancement of biofilm formation is of minor importance. Benzalkonium chloride seems to be the least suitable biocidal active substance, taking into account the often observed strong and stable adaptive response, the cross-tolerance with some other biocidal active substances and the inconclusive effect on biofilm formation and removal.