Abstract: X-ray diffraction, FTIR, and chemical analyses were performed on clay fractions (1–2 µm, <0.1 µm), separated by means of size fractionations and high-gradient magnetic separation techniques, from a Cryorthod developed in a chlorite-mica schist saprolite. Weathering of large phyllosilicates pre-existing in the saprolite involves physical fragmentation and mineralogical transformations. Chloritic minerals in the coarse fractions were the most affected by physical breakdown, while micas were generally preserved. As a consequence, a concentration of mica layers occurred in the coarse clay fraction, while chloritic residues accumulated in the fine clays. These residues exhibited the typical XRD pattern of hydroxy-interlayered intergrade minerals, but the interlayered contaminants were found to be mainly hydroxy-Mg cations. Further mineralogical transformations of the intergrade minerals involved the progressive removal of the hydroxide interlayered sheet and dissolution of chloritic layers. Illite/smectite mixed-layers were formed in the surface horizon of the soil profile. These processes were associated with a strong decrease in Fe and Mg contents in the clay fractions.