Abstract: Method and apparatus for cleaning the internal channels of a medical endoscope wherein the water bottle is replaced with a cleaning bottle adapted to pass fluids stored in the bottle into both the air and the water channels of the instrument. An end cap having a fluid reservoir is placed over the distal end of the instrument. The air/water pump and the suction pump are then cycled to pass a cleaning solution stored in the replacement bottle through the air and water channels into the end cap. The solution in the end cap is drawn through the suction line and collected in a container for disposal. The procedure is repeated using a rinse solution. The pumps are allowed to run after the rinse solution is exhausted, thus air drying the channels.