The small angle X-ray scattering technique was used to probe structural heterogeneity on the scale of nanometers within Nafion(R)/[silicon oxide], Nafion(R)/[ORMOSIL], and Nafion(R)/[dimethylsiloxane] hybrid membranes. The results of this study reinforced the working hypothesis of morphological template action for the tn situ growth of silicon oxide, or organically modified silicon oxide phases in perfluorosulfonate ionomers via sol-gel reactions for silicon alkoxide or/and silicon alkylalkoxide precursors. Nanophase separation persists when incorporated silicon oxide particles are postreacted with ethoxytrimethylsilane but postreaction with diethoxydimethylsilane generates co-continuous phases that do not generate ionomer SAXS peaks, presumably due to a more homogeneous Si atom distribution within the ionomer. These hybrids are true nanocomposites, as structural heterogeneity exists on the scale of similar to 5 nm. The variation of the small angle upturn for these hybrids is explained in terms of long-range inhomogeneities in ionomers.