Polymer nanocomposite membranes based on sulphonated poly(ether ether ketone) (SPEEK) containing different weight percentages of synthetic non-spherical nanofillers such as laponite and MCM-41 were prepared and characterised for direct methanol fuel cells (DMFC). Prior to the preparation of the composite membranes, they were modified using organo silanes. The results showed that there was a decrease in methanol and water permeability with the increasing content of modified laponite and MCM-41. While the membranes containing higher (> 10) weight percentages of silicates displayed lower proton conductivity values than plain polymer, the lower percentages even showed better values than the plain. The results are compared with the membranes containing spherical nanotillers, namely Acrosil and an isotropic silica network system in order to see the effect of shape of nanofillers on the properties of the composite membranes. Among all shapes, membranes containing silica network had the lowest permeability but they also had poor conductivity values. Much more evident than the effect of form or aspect was the influence of the filter surface modification. In all the cases, organic modification drastically decreased methanol and water permeabilities. A good agreement between the experiment and theory was found for the permeability reduction for membranes containing lower weight percentages of layered silicates assuming aspect ratio of 125 for laponite. © 2005 Elsevier B.V. All rights reserved.