We studied by small-angle neutron scattering (SANS) the polymer chain conformation in model silica/polystyrene (PS) nanocomposites. Using the zero average contrast method, we can properly match silica signal to directly measure the form factor of a single PS chain. An important effort has been put to eliminate the silica scattering using two distinct approaches (called respectively “three” and “four” components methods) leading to analogue results. By combining SANS data with small-angle X-ray scattering (SAXS) measurements and transmission electronic microscopy (TEM) images on the same samples, we obtain a very clear result about the effect on polymer chain conformation of the filler dispersion, either at low filler volume fraction, where silica arrange in small aggregates or at higher concentration where it forms a connected network. From SANS the chain conformation in nanocomposites is identical to the one without silica in a large q range illustrating that the chain conformation remains independent of the filler dispersion whatever the silica connectivity or the polymer molecular weight. This result opens the way to a better overview of the polymer chain conformation contribution, especially adsorption or chain mobility modification effects, in the complex mechanical reinforcement mechanisms of nanocomposites. However, at low q, an unexpected shoulder appears in the SANS curves: this effect does not vary in a systematic way neither with chain molecular weight nor with silica concentration. The non reproducibility of these observations could be related to unusual phase separation between normal and deuterated chains.