A method and a system for use of treatment liquids in an apparatus for staining of tissue specimens on microscope slides, wherein the apparatus comprises a plurality of vessels (4) for receiving different liquids for treatment of the tissue specimens, a plurality of tanks (11) for treatment liquids, connecting lines (15) between the tanks and the vessels, a plurality of pumps (13) connected on the connecting lines, and a control unit for control of the apparatus and the liquid treatment by means of a data program, wherein the control unit is arranged for selective control of the relevant pumps (13), so that vessels (4) to be used in a staining process, are filled with liquid (14) at the start of the staining process, and so that the liquid-filled vessels (4) are emptied automatically when they are no longer to be used in the staining process.