Modified Nafion membranes were prepared by charging Nafion 117 membrane with different long-chained counter ions and used for pervaporation of acetic acid-water mixture. It was observed, that the selectivity of Nafion membrane was enhanced by charging with long-chained counter ions. However, it led to a decrease in permeate flux because of decreasing solubility and diffusivity of the membranes. The results of small angle X-Ray diffraction (XRD) measurement of wet Nafion and modified Nafion samples showed that the cluster dimension of the membranes decreased after charging the membrane with long-chained counter ions. The estimation of the pore diameter of the membranes by Kozeny-Carman equation resulted in a similar tendency. Among the modified Nafion membranes, Nafion (C8H17)(4)N+ is concluded to be the most suitable membrane with a flux of 0.18 kg/m(2) h and a selectivity of 243 for the feed concentration of 90 wt.% acetic acid.