An electric power generation system has elements that improve the cold start capability and freeze tolerance of a constituent fuel cell stack cooperate to reduce the amount of water remaining within the passages of the stack. The system includes a purge system that is connectable to the oxidant supply, fuel supply and/or coolant passages upstream of the stack. When the stack is shut down, the stack is disconnected from an external circuit, and purge fluid is transmitted by the purge system through the stack before the stack falls below the freezing point of water. In systems where fuel and/or oxidant streams are humidified prior to entry into the stack, a humidifier bypass system may be provided in place of the purge system. The humidifier bypass system transmits reactant fluid to the stack in fluid isolation from the humidifier, so that the inlet reactant streams are unhumidified.