Abstract: An integrated system for reprocessing contaminated medical instruments, e.g., scopes, surgical instruments, scope accessories, etc. The system includes plural, e.g., four, instrument processing units and a remotely located common controller for effecting the simultaneous control of each processing unit. Each processing unit includes various components, e.g., pumps, solenoids, valves, sensors etc., and a processing chamber. Each chamber is adapted for receiving a medical instrument carrier to which plural medical instrument in need of processing are connected. The controller includes a microprocessor, an associated memory storing a control program, a keyboard, a video display, and a printer. The control program establishes respective protocols of processing steps for effecting the reprocessing of the medical instruments in each of the reprocessing units by the microprocessor controlling the operation of the various components of the processing units via an electrical interface.