The effect of Pt nano-particles size on the microstructure of catalyst layers in a Polymer Electrolyte Fuel Cell is investigated by means of molecular dynamics simulations. The catalyst layer model includes carbon-supported platinum, perfluorosulfonate ionomer (PFSI), hydronium ions and water molecules. Three different Pt nano-particle sizes. i.e. 1. 2 and 3 nm, are studied, and simulations provide visualization of the distinct micro-morphologies of the CL corresponding to each nano-particle size. The results are analyzed using pair correlation functions, showing that different microstructures are obtained for different Pt nano-particle sizes, and also that inclusion of PFSI in the simulations impacts significantly the final configuration of Pt nano-particles. Water molecules are found to distribute near the side chains of PFSI and surface of Pt nano-particles, but far from the graphite surface. Side chains form clusters and exhibit different dispersion toward the Pt surface. The orientations of the side chains in the vicinity of the Pt surface are analyzed in detail. The dispersion of perfluorosulfonate ionomer is found to strongly influence the merging of Pt nano-particles and, consequently, the CL microstructure formation. (C) 2009 Elsevier Ltd. All rights reserved.