As a method for surveying efficient separation conditions for the mobile phase, a 96-well micro-plate based monolithic ion-exchange chromatography system was developed. Discontinuous flow was accomplished by a vacuum manifold. Linear salt gradient elution experiments were carried out with this system and the elution curves were compared with those for monolithic disk column IEC. The normalized gradient slope-the peak salt concentration data for the micro-plate system agreed with those for the monolithic disk column IEC. This system is useful as the liquid volume needed for the experiment is highly reduced, and large amounts of data are obtained quickly.