The casein micelles of cow's milk are polydisperse, more-or-less spherical, protein particles of up to several hundred nanometer in size, containing about 7% by dry weight of calcium phosphate. Small-angle neutron scattering with contrast variation and small-angle X-ray scattering were used in critical tests of models of casein micelle substructure. An inflexion in the neutron scattering curve near Q=0.35 nm⁻¹ was observed in heavy water which became a more pronounced subsidiary maximum at the match point of the protein. In water-rich buffers, where the contrast between protein and calcium phosphate is small, the inflexion was less apparent. The position of the inflexion and its variation in shape and relative importance with contrast matching are explained poorly, if at all, by the submicelle models of casein micelle substructure. However, the observations are explained by a model in which a relatively uniform protein matrix contains a disordered array of calcium phosphate ion clusters. A notable achievement of the model is the prediction of the position of the subsidiary maximum from independent measurements of the intrinsic viscosity of micelles, their mass fraction of calcium phosphate and the mass of the core of a calcium phosphate nanocluster.