Chemical analysis and element mapping of clay-size grains using scanning and transmission electron microscopy (STEM-EDX) greatly facilitates investigations of minor minerals and the location (speciation) of minor elements in the clay fraction. STEM-EDX was used to identify minor minerals and determine the composition of grains in the clay fraction of three soils developed from marble, phyllite, mica-schist and granite in southern Brazil. Before STEM-EDX analysis the clay was treated with citrate-bicarbonate-dithionite or NaOH to remove iron oxides and kaolin respectively. Chemical formulas of clay-size grains were calculated based on EDX analyses. Minerals that were not detected by XRD in the clay fraction were identified from STEM-EDX analyses, including fluorophlogopite, baileychlore, saponite-sauconite, gorceixite and crandallite. Partly weathered (altered) particles of fluorophlogopite had reduced F, K and Mg concentrations. High Zn concentrations in phyllite and mica-schist parent rocks were associated with the presence of baileychlore in the clay. Barium occurred in K-feldspar, smectite and illite. Small amounts of Ti were allocated in octahedral layer of smectite and illite. The chemical analyses of clay size particles supplied by high resolution STEM-EDX has great potential for investigating the location of elements within minerals in the clay fraction.