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In this paper, we demonstrate a Nafion® filled porous silicon membrane with channels as proton exchange membrane (PEM) for micro direct methanol fuel cell (μDMFC). Nafion® filled nano porous silicon membranes with thickness of 60um have proton conductivities (0.02S/cm ~ 0.03S/cm) comparable to the Nafion® membrane (0.05S/cm) which is the most commonly used commercial PEM material. The serpentine channels fabricated by KOH etching are used to provide the fuel and oxygen. Thank to these techniques, a compact structure μDMFC that integrates anode plate, cathode plate and membrane electrode assembly (MEA) on a single layer can be achieved. The new μDMFC based on the nano porous silicon membrane can make the encapsulation and integration with micro electromechanical system easier.