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The structure of polymer nanocomposites has important consequences on final properties, like e.g.mechanical reinforcement. The structure of the hard filler phase is usually characterized by electronmicroscopy and small-angle X-ray scattering (SAXS), and we will review recent examples of fillerstructure in model and industrial nanocomposites. The chain conformation can only bemeasured by small-angle neutron scattering (SANS) with isotopic substitution. Over the past 15 years,considerable efforts have been dedicated to such measurements. Results appear to converge towardGaussian statistics of chains, unperturbed by the presence of filler NPs, and exceptions seem to be dueto system-dependent effects. In nearly all studies, however, unexplained pollution of the scatteringdata in the low-q range has been observed, in spite of careful contrast-matching.In this study, the conformation of polymer chains in silica-latex nanocomposites has been studiedunder zero-average contrast (ZAC) conditions using SANS. Samples have been prepared by dryingcolloidal suspensions of silica and polymer nanoparticles (NPs) for two different silica NPs (radius of5 and 15 nm) and two chain masses (17 and 100 kg/mol). By mixing appropriate amounts ofhydrogenated and deuterated polymer, chain scattering contrast is introduced, and in principle silicascattering is suppressed. However, the SANS scattering intensities displayed distinct deviations at lowangles. Comparison of the SANS and SAXS intensities proves that the measurement of chain structureby SANS is perturbed by unwanted silica contributions, i.e., the silica is ‘mysteriously’ visible. Aquantitative model rationalizing these contributions for the first time is proposed. It is based on astatistical H/D-mismatch in the local environment of the silica NPs. Such a mismatch leads to theexistence of a nanometer-thick polymer shell surrounding silica NPs, which carries H/D contrast andthereby produce an undesired scattering contribution. These shells are presumably maintained by thereduced mobility of polymer close to interfaces or attractive polymer-silica interactions. The effect ofunwanted filler scattering is NP size-dependent − it is pronounced only for smaller beads. This isprobably why ZAC turned out to be so difficult with polymer nanocomposites.