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Both dielectrophoresis (DEP) and flow cytometry are widely applied in microfluidic systems for the handling and measurements of cells and particles. Here, we present a novel integrated microchip, combining a DEP selective filter with flow cytometers for real-time monitoring of the cell sorting processes. The DEP filter was integrated inside a microfluidic channel to sort cells by positive DEP. The cells were hydrodynamically focused to the center of the channel by using a sheath flow from either side. Two flow cytometer (FC) detection windows were set upstream and downstream, respectively, from the DEP filter to measure the forward scattered light of passing cells. Comparing the cell counting rates measured on two different FCs, the collection efficiency of the DEP filter could be determined. This microchip was used to quantitatively monitor the sorting of viable from nonviable yeast cells.