A cartridge holder (30) for an automated endoscope reprocessor (10) is mounted on a movable rack (14). As the rack is wheeled into the chamber, a connector (164) on the cartridge holder (164) automatically makes a fluid connection with a connection port (158) within the chamber. The cartridge holder includes a base (42) and a lid (44), which is pivotally connected to the base by a hinge (110). A cartridge (40) holding a dose of a disinfectant concentrate or reagents is positioned in a well (50) defined by the base and the lid closed. Water flows through the cartridge holder via a fluid passageway (A) defined in part by the lid and in part by the hinge. The water mixes with the concentrate or reagents and the resulting disinfectant solution passes out of a lower end (205) of the cartridge into the well. The solution flows upwardly, around the cartridge, through an annular space (232) between the cartridge and the well, disinfecting the well in the process. The solution exits the cartridge through a plurality of bores (80) at an upper end of the base.