We have developed a technique to fabricate Au microelectrodes on hydrogel substrates such as polyacrylamide. Electropolymerization of poly(3,4-ethylenedioxythiophene) (PEDOT) anchors the Au electrodes to the hydrogels. The resulting soft, molecularly permeable hydrogel-based microelectrodes were effective for the electroporation of adherent cells by direct lamination. The electroporation-assisted uptakes of dye molecules and genes were demonstrated for normal human dermal fibroblast cells and human induced pluripotent stem (iPS) cells.