In practice, the assembly error of the bipolar plate (BPP) in a PEM fuel cell stack is unavoidable based on the current assembly process. However its effect on the performance of the PEM fuel cell stack is not reported yet. In this study, a methodology based on FEA model, "least squares-support vector machine (LS-SVM)" simulation and statistical analysis is developed to investigate the effect of the assembly error of the BPP on the pressure distribution and stress failure of membrane electrode assembly (MEA). At first, a parameterized FEA model of a metallic BPP/MEA assembly is established. Then, the LS-SVM simulation process is conducted based on the FEA model, and datasets for the pressure distribution and Von Mises stress of MEA are obtained, respectively for each assembly error. At last, the effect of the assembly error is obtained by applying the statistical analysis to the LS-SVM results. A regression equation between the stress failure and the assembly error is also built, and the allowed maximum assembly error is calculated based on the equation. The methodology in this study is beneficial to understand the mechanism of the assembly error and can be applied to guide the assembly process for the PEM fuel cell stack. (C) 2010 Elsevier B.V. All rights reserved.