Alumina-coated silica nanoparticles (NPs) grafted with phosphonic acids of different hydrophobicitywere used as filler in poly(ethylacrylate) nanocomposites. Phosphonic acids bearing short alkyl chains ora diethylene glycol group have been grafted at densities up to 3.2 P/nm2 on NPs (20 nm) dispersed inwater. Nanocomposites at particle fractions up to 10 vol% have been formulated by casting from thecolloidal mixtures of modified NPs and nanolatex in water. The dispersion of the NPs in the polymermatrix has been studied by TEM combined with small-angle scattering, evidencing aggregation of NPs.TEM shows micrometer-scale inhomogeneities depending on the surface/polymer matrix compatibility.For the local interparticle correlations, a quantitative analysis of the intensity based on the mapping ontothe effective structure factor of polydisperse hard spheres is developed. This mapping allows the modelfreedetermination of the internal volume fraction of aggregates, termed compacity k, to between 10%and 30%, compatible with the TEM analysis. k is found to increase for the higher particle volume fractions,to decrease with grafting density, and to be mostly independent of the nature and mass of thegraft. Preliminary evidence for an improved compatibility of grafted with respect to bare NPs is found, asopposed to their aqueous precursor suspensions where some pre-aggregation is induced by grafting.