A method of controlling the temperature within an electrochemical fuel cell stack comprises introducing a reactant fluid stream comprising both a heat transfer liquid and a reactant into a fuel cell assembly such that the reactant fluid stream contacts an electrode. The heat transfer liquid is other than water. Preferably, the method further comprises recirculating heat transfer liquid which is in the reactant exhaust stream, typically via a heat exchanger, and re-introducing it into the fuel cell assembly in the reactant fluid stream. The recirculated heat transfer liquid may be directed to a reservoir which in turn supplies heat transfer liquid to the reactant fluid stream as it is needed. In a further embodiment, the method may comprise using the heat transfer liquid to heat a fuel cell stack to a desired operating temperature rather than cooling the stack.