Magnetic ion-conducting nanoparticles were prepared for application in polyelectrolyte membranes. The surface of gamma-Fe2O3 nanoparticles is modified via silanation reaction and then by oxidation of the terminal mercapto groups to make functional sulfonate groups. The modified nanoparticles are characterized by using Fourier transform infrared spectroscopy (FT-IR), thermogravimetric analysis (TGA), scanning electron microscopy-energy dispersive X-ray spectroscopy (SEM-EDS) and vibrating sample magnetometer (VSM). Afterward, by applying the magnetic field during solvent casting and evaporation, Polyelectrolyte membranes are prepared based on Nafion and gamma-Fe2O3 nanoparticles with oriented microstructure. Under such conditions, the subjected magnetic field induced nanoparticles form long chains extending across the membrane. By clustering sulfonate groups of Nafion around aligned nanoparticles, a short path length for proton transportation is achieved and leads to increase in proton conductivity. Effects of sulfonation and also ordering of the particles on swelling property, proton conductivity, activation energy, methanol permeability and selectivity are investigated. Nanocomposite membranes with oriented microstructure, due to high proton conductivity and low methanol permeability, displayed significantly enhanced selectivity in comparison with membranes with randomly distributed nanoparticles. This new type of proton exchange nanocomposite membranes could be considered as electrolytes for use in hydrogen or direct methanol fuel cells. (C) 2012 Elsevier B.V. All rights reserved.