The microstructural evolution and swelling behaviors of sulfonated poly(etheretherketone) (SPEEK) and Nation polymer membranes have been investigated by small angle X-ray scattering (SAXS) after equilibrating them in 2 M methanol solution at various temperatures, which is relevant for their use in direct methanol fuel cells (DMFC). The relationships among Bragg distance, sulfonation levels of the membrane, equilibrating temperature and transport properties are discussed. The proton conduction properties of the SPEEK and Nation membranes have been investigated by electrochemical impedance spectroscopy. The network cluster model is employed to retrieve the structural information from the scattering and proton conductivity data. While the SPEEK membranes have narrower pathways for methanol/water permeation at T < 70 degrees C, the Nafion membranes have a wider channel even at lower temperatures, resulting in a higher methanol permeability in the latter. Based on the differences in the structural/cluster evolutions, the advantages and limitations of the two polymer membranes for use in DMFC are discussed. (c) 2005 Elsevier B.V. All rights reserved.