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We present a novel flow-type single cell electroporation (SCE) system for low voltage electroporation of biological cells. We have used a microfabricated silicon sense-porate aperture to detect and identify a cell by its impedance and then apply the optimum electric field on it. Incorporation of a fluorescent dye into mouse embryo fibroblast NIH-3T3 cells has been demonstrated with a cell survival rate or viability much higher than conventional macro-electroporators. This paper reports the principle, design and implementation of this system and the experimental results obtained using it.