An unambiguous identification of pigments in paint layers of works of art forms a substantial part of the description of a painting technique, which is essential for the evaluation of the work of art including determination of the period and/or region of its creation as well as its attribution to a workshop or an author. Copper pigments represent a significant group of materials used in historic paintings. Because of their substantial diversity and, on the other hand, similarity, their identification and differentiation is a challenging task. An analytical procedure for unambiguous determination of both mineral-type (azurite, malachite, posnjakite, atacamite, etc.) and verdigris-type (copper acetates) copper pigments in the paint layers is presented, including light microscopy under VIS and UV light, electron microscopy with elemental microanalysis, Fourier transformed infrared micro-spectroscopy (micro-FTIR), and X-ray powder micro-diffraction (micro-XRD). Micro-Raman measurements were largely hindered by fluorescence. The choice of the analytical methods meets the contemporary requirement of a detailed description of various components in heterogeneous and minute samples of paint layers without their destruction. It is beneficial to use the combination of phase sensitive methods such as micro-FTIR and micro-XRD, because it allows the identification of both mineral-type and verdigris-type copper pigments in one paint layer. In addition, preliminary results concerning the study of the loss of crystallinity of verdigris-type pigments in proteinaceous binding media and the effect of lead white and lead tin yellow as highly absorbing matrix on verdigris identification in paint layers are reported.