This paper studies the optimization method of channel geometries for a proton exchange membrane fuel cell (PEMFC) using a genetic algorithm (GA). The channel and rib widths and channel height are selected as geometry variables. The fuel cell output power is chosen as the cost function for the optimization. In this paper, an in-house genetic algorithm is constructed, and the fuel cell output power is obtained using an interfacing program connected to a commercial computational fluid dynamics (CFD) tool, COMSOL, in a Matlab environment. The 2D PEMFC is used to calculate the performance cost function for computational time and cost. The calculated output power of the PEMFC is delivered to the in-house GA program to check for optimality. After the optimality is checked, the new geometry data is fed back to the COMSOL to calculate the PEMFC output power until the optimization process is finished. Experiments are conducted to support the optimized results using three different channel geometries: channel-to-rib width ratios of 0.5:1, 1:1, and 2:1. A full 3D PEMFC CFD model is constructed using COMSOL to support the 2D CFD optimization results. This paper shows the possibility of applying the geometry optimization process to sophisticated electrochemical reaction systems, such as a PEMFC, using a GA and a commercial CFD tool on the Matlab platform. The geometries and materials can be optimized using this approach to obtain the most efficient performance of an electrochemical system. Copyright (C) 2014, Hydrogen Energy Publications, LLC. Published by Elsevier Ltd. All rights reserved.