The invention relates to the use of agents, which contain at least one disinfection system based on selected organic peracids and combinations of peracids, in automatically functioning systems, in which fragile medical appliances, in particular, endoscopes, are cleaned and disinfected. According to the invention, the appliances are brought into contact with an aqueous disinfection agent solution after they have been treated and/or at the same time they are being treated with an aqueous cleaning solution. The invention also relates to cleaning and disinfection agents and methods which are all suited for carrying out this purpose.