A system for decontaminating a medical device such as an endoscope comprising a chemical chamber configured to dispense a decontaminant therein as a fog, a decontamination chamber configured to retain the medical device and receive the fog from the chemical chamber, a pressure control assembly for said decontamination chamber to manage pressure and fluid flow between the chemical chamber and the decontamination chamber and an enclosure, such as a pouch, for retaining the medical device comprising a fog-permeable layer and an exterior port member to interface with the decontamination chamber to transfer the fog from the chemical chamber into the enclosure.
