We have improved the design of compartmental electrophoresis apparatus. Gel casting has been made very quickly and simply by employing perspex plugs which screw into wax casting cylinders. The apparatus has been automated by connecting an electronic circuitry to a peristaltic pump which keeps the levels and pH of buffers constant in anodic and cathodic chambers. A water jacket has also been added to the apparatus. This vastly improved version of compartmental electrophoresis apparatus could now be successfully used for the separation of noncovalently linked polysaccharides from any protein or enzyme.