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In this study, a DEP chip with multi-layer electrodes and microcavities array was designed for trapping cells and further impedance measurement. The capability of trapping cells can be achieved single-cell level and without overlapping due to the effects of SU-8 microcavities. However, the depth of microcavity also could affect the results of impedance measurement owing to the insulation layer of SU-8. Two kinds of DEP chip with different thickness of SU-8 layer were, therefore, fabricated and performed to investigate the microstructural effects on impedance measurement. By using this microchip, we can easily identify whether cells (HL-60) are uptaken of Au nanoparticles or not according to the impedance spectrum. Consequently, this method provides an alternative way to separate normal cells and cells uptake of nanoparticles for further inspection.