Abstract.Topsoil (0–20 cm) and subsoil (60–100 cm) properties are compared at agricultural and nearby natural vegetation sites in São Paulo State. Differences are related to land use and climate, in order to estimate soil carbon storage under various ecosystems and also to study the effects of high‐input agriculture on the chemical composition of soils with low activity clays. Within each land use, organic carbon in the topsoil is most strongly related to clay + silt content. This relationship is stronger for cropped, short savannah (cerrado) and tall savannah (cerradão) sites than for semi‐deciduous and evergreen forest sites. Losses of topsoil carbon with cropping can be predicted if the initial carbon and the clay+silt contents are known. The greatest carbon losses after long term cultivation occurred in forest mineral topsoils, ranging from 6% for perudic clayey soils to 37% for ustic sandy soils. No significant difference in carbon content was found between the paired savannah‐cultivated sites. In most of the originally less fertile soils cation exchange capacity was greater in the cultivated topsoil (Ap) than in the topsoil under savannah or forest (A1), probably because of liming and phosphate fertilization. Most subsoils at agricultural sites show increases in exchangeable bases (mainly Ca) and base saturation, but no significant c