The invention concerns a medical instrument disinfecting system (1) comprising a disinfecting chamber (4) adapted to implement a cycle for disinfecting the instruments. The invention is characterized in that each instrument (1) comprises identification data (5) and in that the chamber (4) is associated with means (6) for acquiring the identification data of the or each instrument (1) when it is introduced into or withdrawn from the chamber (4) at the start and at the end of a disinfecting cycle, with means (7, 8) for acquiring characterization data of the disinfecting cycle and with means (9, 10, 11, 12, 13) for associating the identification data of the or each instrument and the characterization data of the disinfecting cycle to generate traceability data of the disinfection of the or each instrument.
