Paint cross-sections have been analysed using the attenuated total reflection technique combined with FTIR mapping microspectroscopy in order to characterise the nature of the compounds present and map their localisation in the stratigraphy. The study reveals the possibilities offered by micro-ATR devices for obtaining informations about the organic substances employed in painting techniques and in particular their distribution in the different layers, showing a real improvement over traditional analytical investigations in use for the detection of organic substances. Limitations, such as the contamination of the embedding resin and the typical spectral resolution (20 microm) are presented and alternative methods were proposed to obtain better results. In particular, the use of an infrared transparent salt (KBr) as embedding material for the cross-sections is evaluated and seems to be very promising. Furthermore, ATR mapping represent a useful non-destructive analytical technique complementary to others molecular and elemental analyses to be performed afterwards such as SEM-EDX.