In automated reprocessing system (B), a leak detection system (10) evaluates the integrity of an endoscope (A), having an internal passage (66). The leak detection system includes an interior chamber (42) which is connected to the internal passage by quick connects (18, 20). A source of compressed air (22) pressurizes the chamber and internal passage to a suitable test pressure. A pressure sensor (50) and a temperature sensor (54) detect the pressure and temperature within the chamber and hence in the endoscope passage. Pressure and temperature measurements made over time are used to determine changes in the gas volume, indicative of whether leaks are present in the endoscope. If the endoscope is determined to be free of leaks, the endoscope is washed and microbially decontaminated in the reprocessing system. During the decontamination process, the pressure within the internal passage is maintained in a range at which ingress of fluid is avoided yet the endoscope is not subjected to a potentially damaging pressure.