Analytical transmission electron microscopy (ATEM) has been applied to ultra-thin sections of Quattrocento Italian paintings samples. Ultra-thin sections (100 nm) were obtained from painting microsamples by diamond-knife ultramicrotomy after embedding and impregnation by Spurr mixture (chemically ultrapure Epoxy Resin). These sections are transparent to electrons, and single pigment grains can be analyzed by ATEM. This method gives simultaneously, for each micrograin well localized in the stratigraphic section: morphology and granulometry by transmission electron microscopy (TEM); elemental composition by X-ray energy dispersive spectrometry (EDS); and, crystalline paraments used by two Quattrocento Italian Painters has been carried out. Emphasizes <i>in situ</i> distinction of the two polymorphic chemical species of copper carbonate, azurite and malachite; in situ characterization of the two types of lead-tin yellow. Mineralogical standards (natural and/or synthetic) have been prepared previously and analyzed according to the same procedures, for calibration of the methods, especially electron micro-diffraction.