A method for cleaning/sterilizing a medical device with a lumen comprises the steps of: a) providing a container having one enclosure and one openable and closeable interface separating the container and the enclosure, b) placing the device on a tray, c) placing the tray into the container and enclosure so that one end of the device and a portion of the tray are located in the container and the other end of the device and another portion of the tray are located in the enclosure, d) creating a pressure difference between the two ends, e) cleaning the device with a cleaning solution, f) rinsing the device with rinse solution, g) treating the device with a chemical germicide. An apparatus for cleaning/sterilizing a device with a lumen comprises a container having at least two separated close compartments. An openable and closeable interface separates the container into the compartments. A tray is adapted to be placed in the two compartments crossing the interface for accommodating the device, so that one end of the device is in one compartment and the other end is in the other compartment. A source for creating a pressure difference is provided. A cleaning mechanism adapted to clean the device is also provided.