The stability and mechanism underlying the formation of deposits of casein micelles during ultrafiltration process were investigated by small-angle and ultra small-angle x-ray scattering ~SAXS and USAXS. The casein micelle dispersions consisted of phospho-caseinate model powders and the measurements probed length scales ranging from 1 to 2000 nm. Rheometric and frontal filtration measurements were combined with SAXS to establish the relationship between the rheological behavior of deposits (shear and/or compression) and the corresponding microstructure. The results revealed two characteristic length scales for the equilibrium structure with radius of gyrations Rg , about 100 and 5.6 nm pertaining to the globular micelles and their non-globular internal structure, respectively. The SAXS measurements further indicated that the increase of temperature from 20 to 70 °C or the decrease of pH from 6.6 to 6 lead to agglomeration of the globular micelles. In situ scattering measurements showed that the decrease of permeation flows is directly related to the deformation and compression of the micelles in the immediate vicinity of the membrane.