The design of the flow field greatly affects the flow distribution and the final performance of the proton exchange membrane fuel cell (PEMFC) system. The clamping force between the gas diffusion layer (GDL) and the flow field plate (FFP) will cause the inhomogeneous compression of the GDL Then the GDL will be intruded into the reactant gas channels and eventually change the flow distribution. This paper presents a study on the effect of the intrusion of the GDL on the flow field in a PEMFC, and tries to explain the reason for poor performance of the previous design of the flow field other than those have been studied in other papers such as GDL roughness, porosity, etc. First of all, a linear analytical model is used to analyze the sensitivities of the flow field to the GDL intrusion, and then used to estimate the effect of the GDL intrusion on the flow field distribution. Secondly, a multi-objective optimization model is proposed to eliminate the nonuniform distribution in the flow field with the GDL intrusion taken into consideration. Subsequently, three different designs are analyzed and compared with each other as a demonstration to show the effect of the GDL intrusion. From the analysis results, it is recommended that the effect of the GDL intrusion on the multi-depth flow field should be taken into consideration and the flow field should be insensitive to the GDL intrusion to obtain high robust performance. The results obtained in the study provide the designer some useful guidelines in the concept design of flow field configurations. (C) 2010 Elsevier Ltd. All rights reserved.