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This paper presents a fabrication process that allows the integration of three dimensional (3D) bulk silicon electrodes and planar gold electrodes in a PDMS microfluidic system. This process: i) uses widely available technologies and is easily machinable and applicable to mass production; ii) possesses superior optical properties to allow facile monitoring during analysis; and iii) is compatible with silicon based sensors. One target application is electric impedance spectroscopy (EIS) on biological samples. Bipolar and tetrapolar measurements have been performed on saline solutions. The robustness and the geometry of the electrodes allow us to envision various applications for sensor devices or electrical bio-cells manipulation or engineering such as electrokinetics or electroporation.