To provide a medical device cleaning and disinfecting system which can remove the burden of cleaning and disinfecting an endoscope having a conduit and allow cleaning and disinfecting to be performed hygienically after use.

A medical device cleaning and disinfecting system 1 comprises an endoscope 20 which has opening sections 25g and 25h of a plurality of conduits 25a and 25b including a suction conduit 25c on a base part 21 and a cleaning and disinfecting device 2 which has a cleaning bath 5 and a plurality of conduit cleaning nozzles 31, 32, and 33 and cleans and disinfects the outer surface of the endoscope 20 and the inside of a plurality of conduits 25a, 25b, and 25c after use. Among a plurality of the opening sections 25g and 25h formed on the base part 21 of the endoscope 20, at least the opening section 25g of the suction conduit 25c is formed independently with a specified distance away from the opening section 25h of the other conduits 25a and 25b, and a cleaning nozzle attaching and detaching mechanical section 30 which automatically attaches and detaches a plurality of conduit cleaning nozzles 31, 32, and 33 formed on the cleaning and disinfecting device 2 to and from each of the opening sections 25g and 25h of the base part 21.