The aim of the present research was to study the clay mineralogy and vertical patterns of clay mineral distribution in the well-drained, shallow and stony soils underlain by solid rocks from the different regions of Siberia. The solid rocks were represented by traprocks of the Central Siberian plateau and limestones of south Siberia (the Baikal region). The studied soil profiles developed from the fine earth of traprocks and red colored calcareous substrate, correspondently. The scheme of traprocks conversion into a clay-rich matrix within inherited smectite forming the secondary plasma in the acidic soil environment was discussed. The data increased the knowledge concerning the schemes of weathering and pedogenesis from the solid silicate rocks. Besides the specificity of pedogenesis and soil clay mineralogy on the red colored calcareous substrate of the Baikal region comparing with the soils on the Permian calcareous and red colored sediment from European Russia was elucidated.