This disinfection system for medical instruments of the type comprising a disinfection chamber adapted to implement a cycle for disinfecting instruments, is characterized in that each instrument is associated with a radiofrequency label containing identification information and in that the chamber is associated with radiofrequency means for acquiring identification information about the or each instrument when put in place and removed from the chamber at the start and end of a disinfection cycle, with means of acquiring information characterizing the disinfection cycle and with means for combining identification information about the or each instrument with information characterizing the disinfection cycle in order to generate traceability information on the disinfection of the or each instrument.