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This paper presents an embedded frequency response analyzer for fuel cells (FCs) based on a robust measurement technique with simple implementation. A frequency response analysis technique provides valuable information of different electrochemical processes that occur inside the FC. The measurement system is implemented on a low-cost digital signal processor to perform frequency response and impedance tracking. The small-size and low-power consumption allows this special device to be embedded into the FC controller or power conditioning stage. The system is capable of measuring automatically the frequency response of the FC at different operating points, even when the FC is operating with a load. These measurements can be used to characterize the FC at the design stage and to perform online monitoring of the FC state during a continuous operation. The proposed instrument uses the lock-in amplification technique, which allows very accurate and precise measurements even in the presence of high noise levels. The proposed hardware and signal processing technique are described in this paper, including the experimental result of a 1.2-kW proton exchange membrane FC system.