Nafion nanocomposite membranes were prepared from Nafion 117 and a systematic range of organically functionalized silicon alkoxide precursors using an in situ sol gel synthesis technique. The physical structure of the resulting nanocomposite membranes were characterized using small and wide-angle X-ray scattering, small angle neutron scattering, positron annihilation lifetime spectroscopy, and transmission electron microscopy. A structural model is proposed for three typical nanocomposite membranes (Nafion-TEOS, Nafion-MPTMS and Nafion-MPMDMS). The proton and methanol transport properties of the membranes included in the model were evaluated by impedance spectroscopy and pervaporation experiments, respectively, and correlated to their composite microstructure. In particular, this model explains the increased selectivity for transport over protons for nanocomposite membranes produced using (3-mercaptopropyl)methyldimethoxysilane as the silicon alkoxide precursor, which is more than six times higher than that of Nafion 117. © 2007 American Chemical Society.