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Water content estimation is a key problem for studying the PEM fuel cell. When several hundred fuel cells are connected in serial and their active surface area is enlarged for sufficient power, the difference between cells becomes significant with respect to voltage and water content. The voltage of each cell is measurable by the cell voltage monitor (CVM) while it is difficult to estimate water content of the individual. Resistance of the polymer electrolyte membrane is monotonically related to its water content, so that the new online high frequency resistance (HFR) measurement technique is investigated to identify the uniformity of water content between cells and analyze its sensitivity to operating conditions in this paper. Firstly, the accuracy of the proposed technique is experimentally validated to be comparable to that of a commercialized electrochemical impedance spectroscopy (EIS) measurement equipment.