Methanol crossover, mainly due to diffusion mechanism, deteriorates the performance of direct methanol fuel cells. Using a molecular simulation technique, we try to reproduce the methanol diffusion event in a model Nafion membrane with an atomistic resolution. The simulation system comprises molecules of the Nafion-water-methanol-hydronium ions at four different concentrations of methanol. Molecular simulation results show that methanol molecules migrate with water clusters and hydronium ions via the sulfonic acid groups of the side chains of the electrolyte. Electro-osmotic drag coefficients and diffusion coefficients of methanol were evaluated at varied methanol concentration and compared to reported experimental results. The thermal effect on the methanol diffusion was also investigated using this molecular analysis technique. (c) 2008 The Electrochemical Society. [DOI: 10.1149/1.2987878] All rights reserved.