Perfluorosulfonated ionomer (PFSI) was synthesized and PFSI membranes were prepared via a solution-cast method and annealed at different temperatures from 150 to 230 degrees C. The annealing effect on water content, proton conductivity, and methanol permeability were reported and discussed. X-ray diffraction and small angle X-ray scattering were used to test the structure of the membranes. It was found that annealing increased the proton conductivity of the membranes because heat-treatment helped to free the sulfonic groups that were buried in the polymer segments and form more organized ionic clusters. Water content and methanol permeability of the annealed membranes decreased with increasing annealing temperature. Simultaneously, annealing induced more compact chain packing structure, which eventually affected the transport of the proton and methanol through these ionomer membranes. (C) 2007 Wiley Periodicals, Inc.