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Throughput in the cell response analysis is expected to progress in medicine and biology. In this paper, we construct a method for the measurement of cell activity that is measured by the pH fluctuation of the solution around the cell. To improve throughput of the measurements, first we constructed an automatic pH measurement system using ion-sensitive field-effect transistor (ISFET), and the system composed of 96-well microplate, pump, XYZ stage, and PC. The basic data of the cell activity was taken from human embryonic kidney 293 (HEK 293) cells by the use of flow-through type measuring chamber.