The invention provides a fuel cell system that is free from troubles due to contaminant ions by controlling the concentration of contaminant ions in cooling water. The fuel cell system comprises a fuel cell stack and a means for controlling the cell temperature by circulating a liquid coolant in the fuel cell stack or bringing it in contact with the fuel cell stack, the fuel cell stack comprising a plurality of unit cells that are laid one upon another, each of the unit cells comprising a hydrogen ion-conductive electrolyte membrane, a pair of gas diffusion electrodes which sandwich the electrolyte membrane, an anode-side conductive separator plate having a gas flow path for supplying a fuel gas to one of the electrodes, and a cathode-side conductive separator plate having a gas flow path for supplying an oxidant gas to the other of the electrodes, wherein a material adsorbing or absorbing ions is provided on a portion of the fuel cell system to come in contact with the liquid coolant.