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Silicon micro-hole arrays (Si-MHA) were fabricated as a gas diffusion layer (GDL) in a micro fuel cell using the micro-electro-mechanical-systems (MEMS) fabrication technique. The resistance temperature detector (RTD) sensor was integrated with the GDL on a bipolar plate to measure the temperature inside the fuel cell. Experimental results demonstrate that temperature was generally linearly related to resistance and that accuracy and sensitivity were within 0.5 °C and 1.68×10-3/°C, respectively. The best experimental performance was 9.37 mW/cm2 at an H2/O2 dry gas flow rate of 30/30 SCCM. Fuel cell temperature during operation was 27 °C, as measured using thermocouples in contact with the backside of the electrode. Fuel cell operating temperature measured in situ was 30.5 °C.