An endoscope processor, according to the present invention, provides for cleaning and sterilizing an endoscope having a body, and a first flexible tube attached to the body. It includes an operational housing and an enclosure which is attachable to and detachable from the operational housing, the enclosure being sealed from ingress of potentially contaminating microorganisms when detached from the operational housing. The enclosure is shaped, sized and oriented to receive the endoscope in an orientation with the first flexible tube depending vertically downwardly from the endoscope body. The enclosure includes a liquid inlet and a liquid outlet. The operational housing includes a circulating system comprising at least one liquid pump having a pump outlet connected to the liquid inlet of the enclosure when the enclosure is attached to the operational housing, and a pump inlet connected to the liquid outlet of the enclosure when the enclosure is attached to the operational housing, whereby to circulate liquid through the enclosure. A source of sterilizing fluid is associated with the pump and a control system is programmed to control a sterilization procedure whereby the pump circulates a liquid comprising the sterilizing fluid through the enclosure.