Effects of heterogeneous surface of commercial gas diffusion layers (GDLs) which is made from carbon papers on a droplet transport in microchannels of proton exchange membrane fuel cells are investigated using the volume of fluid method. A random function is used for generating the heterogeneous surface of GDL in terms of roughness density and roughness height, which is derived from experimental data of commercial carbon paper GDLs. Surface tension, and wall adhesion forces are applied by using the volume of fluid method. The hydrophilic walls and hydrophobic GDL are considered. Results show that the heterogeneous surface of GDLs greatly affects droplet transport in the mircochannels. The movement mechanism of large droplet is translational while rolling mechanism is dominant for small droplet movement. Pressure drop and pressure fluctuation of large droplet are reduced after the formation of film flow. Generally, time-averaged pressure drop, droplet elongation, and the amount of remaining water on the GDL increase by increasing roughness density and roughness height, which is undesirable for better water management. It is also observed that the amount of adhered droplet to the hydrophilic surface of microchannel increases by increasing the roughness height and airflow velocity, which is favorable for better water removal. Average velocity of the droplet decreases by increasing roughness parameters for low airflow velocities while it increases for high airflow velocities. The detachment velocity of droplets on the rough GDL is compared with analytical solution for smooth GDLs. Copyright (C) 2015, Hydrogen Energy Publications, LLC. Published by Elsevier Ltd. All rights reserved.