Various methods of preparation of epoxy resin/clay mixtures, before the addition of the crosslinking agent and curing to form epoxy-based polymer layered silicate (PLS) nanocomposites, have been investigated to determine their effect on the nanostructure. Organically modified montmorillonite clay was used, and the mixtures were prepared by both simple mixing and solvent-based methods. X-ray diffraction shows that intercalation of the resin into the clay galleries occurs for all clay loadings up to 25 wt % and for both preparation methods, but the dispersion of the clay in the resin, observed by optical microscopy, is significantly better for the solvent preparation method. Differential scanning calorimetry (DSC) shows that the intercalated resin has the same molecular mobility as the extra-gallery resin, but suggests that the intercalated resin does not penetrate completely into the galleries. Prolonged storage of the resin/clay mixtures at room temperature leads to changes in the DSC response, as well as in the response to thermogravimetry, which are interpreted as resulting from homopolymerization of the epoxy resin, catalyzed by the onium ion in the modified clay. This confirms and explains the earlier observation of Benson Tolle and Anderson (J Appl Polym Sci 2004, 91, 89) that "conditioning" of the resin/clay mixtures at ambient temperature has a significant effect when the crosslinking agent is subsequently added, and indicates that the preparation method has important consequences for the nanostructure development in the PLS nanocomposites. (c) 2006 Wiley Periodicals, Inc.