In the present study, the simplified conjugate-gradient method (SCGM) is combined with commercial CFD code to build an optimizer for designing the baffles locations with interdigitated channels of a centimeter-scale proton exchange membrane fuel cell (PEMFC). Using the optimizer, the locations of the baffles are adjusted toward the maximization of the average current density of the flow field. The approach is developed by using the commercial CFD code as the direct problem solver, which is able to provide the numerical solutions for the three-dimensional mass, momentum and species transport equations as well as to predict the electron conduction and proton migration taking place in a PEMFC. Results show that the optimal design process of the locations of the baffles can be completed by using the present optimization approach in just a finite number of iterations. The optimization process may lead to an appreciable increase by 14% in the power output from the fuel cell. (C) 2009 Elsevier Ltd. All rights reserved.