A three-dimensional numerical model is developed to investigate and compare the performance of humidifiers with counter-flow and parallel-flow configurations. This model has a set of coupled equations including conservations of mass, momentum, species and energy. The results indicate that in counter-flow humidifier, water and heat transfer is more than that of the parallel-flow that leads to a higher dew point at dry side outlet, consequently, a better humidifier performance. An increase in temperature and a decrease in mass flow rate at dry side inlet lead to a better humidifier performance. However at the low flow rates the humidifier performance does not change a lot by preheating the inlet dry gas. An increase in relative humidity at dry side inlet does not offer any advantage. Copyright (C) 2014, Hydrogen Energy Publications, LLC. Published by Elsevier Ltd. All rights reserved.