A system provides for high level disinfection or sterilization of an endoscope having a first portion adapted for immersion and a second portion not adapted for immersion. The system includes a container having a first basin sized and adapted to receive the first portion of the endoscope for immersion, a separate and adjacent second basin sized and adapted to receive the second portion of the endoscope, a wall between the first basing and the second basin, and a trough in an upper portion of the wall between the first basin and second basin through which a tube connecting the first portion of the endoscope and the second portion of the endoscope may extend.
