The present invention provides a method and apparatus for sanitizing a device, such as an endoscope, having a lumen. The method comprises a) providing a container possessing two or more openings, and a flexible, gas-impermeable pouch that surrounds the container; b) placing the device into the container; c) applying a reduced pressure to the container and pouch, thereby causing the pouch to collapse around the container and form at least one interface separating the container into two or more compartments, which interface is formed under reduced pressure by the adherence of the pouch onto itself and around part of a surface of the device, through openings in the container, such that one end of the device is located in one of the compartments and the other end is in another compartment; and d) generating a flow of a sanitizing solution through the lumen to sanitize the inner surface of the device.