Correct identification of pigments and all accompanying phases found in colour layers of historical paintings are relevant for searching their origin and pigment preparation pathways and for specification of their further degradation processes. We successfully applied the analytical route combining non-destructive in situ X-ray fluorescence analyses with subsequent laboratory investigation of micro-samples by optical microscopy, scanning electron microscopy/energy-dispersive spectroscopy and X-ray powder micro-diffraction (micro-XRD) to obtain efficiently all the data relevant for mineralogical interpretations of the copper pigments origin. Cu salts (carbonates, chlorides, sulphates, etc.) used as pigments exist in a range of polymorphs with similar or identical composition. The efficiency of the micro-XRD for direct identification of such crystal phases present in micro-samples of colour layers was demonstrated in the presented paper. A new, until now unpublished, type of copper pigment--cumengeite, Pb(21)Cu(20)Cl(42)(OH)(40)--used as a blue pigment on a sacral wall painting in the Czech Republic was found by means of micro-XRD. Furthermore, azurite, malachite, paratacamite, atacamite and posnjakite were identified in fragments of colour layers of selected Gothic wall paintings. We found Cu-Zn arsenates indicating the natural origin of azurite and malachite; artificial malachite was distinguishable according to its typical spherulitic crystals. The corrosion of blue azurite to green basic Cu chloride was clearly evidenced on some places exposed to the action of salts and moisture-in a good agreement with the results of laboratory experiments, which also show that oxalic acid accelerates the corrosion of Cu pigments.