FT Raman spectroscopy and micro-Raman spectroscopy with lasers of three different wavelengths (1064 nm, 785 nm and 532 nm) were used for analysis of reference samples of natural clay pigments including white clay minerals (kaolinite, illite, montmorillonite), green earths (glauconite and celadonite) and red earths (natural mixtures of white clay minerals with hematite). In addition, eight micro-samples obtained from historical paintings containing clay pigments in ground and colour layers have been examined. Powder X-ray diffraction and micro-diffraction were used as supplementary methods. It was found that laser operating at 1064 nm provided the best quality Raman spectra for distinguishing different white clay minerals, but the spectra of green and red earths were affected by strong fluorescence caused by the presence of iron. Green earth minerals could be easily distinguished by 532 or 785 nm excitation lasers, even in small concentrations in the paint layers. On the other hand, when anatase (TiO2) or iron oxides (such as hematite) were present as admixtures (both are quite common, particularly in red earths), the collection of characteristic spectra of clay minerals which form the main component of the layer was hindered or even prevented. Another complicating factor was the fluorescence produced by organic binders when analysing the micro-samples of artworks. In those cases, it is always necessary to use powder X-ray micro-diffraction to avoid misleading interpretations of the pigment's composition. Copyright © 2013 John Wiley & Sons, Ltd.