A decontamination system (2) suitable for cleaning and disinfecting a medical instrument (26) such as an endoscope, the system comprising: (I) a plurality of pre-clean wipes for wiping an instrument to be decontaminated each pre-clean wipe comprising a moist fabric member in its own sealed container (4); (II) a two-part disinfectant system comprising: (a) a first part comprising a first reagent in a carrier medium; and (b) a second part which is miscible with the first part and which comprises a second reagent in a carrier medium; wherein the first reagent and the second reagent will react when mixed to provide a disinfecting composition; the first part being contained in a dispenser (6) whereby it will be dispensed as a fluid when the dispenser is actuated, and the second part being absorbed or impregnated in a plurality of disinfecting wipes (30) each of which comprises a fabric member (30) in its own sealed container (8); and (III) a plurality of rinse wipes, each rinse wipe comprising a moist, sterile, fabric member in its own sealed container (10); characterized in that each pre-clean wipe container (4) is provided with a machine-readable Pre-Clean Wipe data carrier (36) which includes data specific to the pre-clean wipe; the dispenser (6) is provided with a machine-readable Dispenser data carrier (58) which includes data specific to the first part; each disinfecting wipe container (8) is provided with a machine-readable Disinfecting Wipe data carrier (44) which includes data specific to the disinfecting wipe (30); and each rinse wipe container (10) is provided with a machine-readable Rinse Wipe data carrier (50) which includes data specific to the rinse wipe.