In this work non-invasive reflection infrared spectroscopy was used to discriminate between different Cu-based green pigments (namely, malachite, verdigris, chrysocolla, emerald green and phthalo green). The pigments, chosen because of their historical widespread use in artworks, were investigated as pure powders and in situ on painted models by reflection FTIR spectroscopy. The distortion arising as a result of the specular and diffuse component of reflected radiation was evaluated as function of the optical and surface properties of the investigated mock-ups. Use of the Kramers-Kronig (KK) algorithm to correct for the distortion arising from the surface reflection gave k index maxima shifted by more than 20 cm(-1) relative to those obtained in conventional transmission mode. These findings stress the need to carefully manage use of the KK algorithm on reflection spectra to avoid erroneous assignment. On the other hand, combination and overtone bands (which are enhanced by the diffuse reflection) were proved to enable reliable and sensitive identification of most of the pigments studied. Knowledge acquired by study of pure compounds and painted models was subsequently applied to interpret the spectra acquired from paintings and manuscripts.