In this paper, a series of Nafion composite membranes with improved methanol barrier properties were fabricated from chitosan (CS) and silicotungstic acid (SiWA) by Layer-by-layer (LbL) self-assembly technique. The Fourier transform infrared attenuated total reflection (FTIR-ATR) spectra and scanning electron microscope (SEM) were employed to prove the successful deposition of CS/SiWA layers. The effect of the methanol-blocking layer on proton conductivity, methanol permeability and direct methanol fuel cell (DMFC) performance was studied. Both proton conductivity and methanol permeability of Nafion composite membranes decreased with the increase of CS/SiWA bi-layer number. The Nafion composite membrane with a reduced proton conductivity of 22% showed a reduced methanol permeability of 47%. Approximate 18% improvement of the selectivity was achieved as compared with plain Nafion membrane. But it did not result in better DMFC performance than that of plain Nafion membrane. Copyright (C) 2012, Hydrogen Energy Publications, LLC. Published by Elsevier Ltd. All rights reserved.