Laser irradiation may alter the colour of certain pigments used in artworks. Owing to the increasing use of lasers in artwork conservation, this problem becomes extremely crucial especially in the case of a polychromy covered by environmental encrustation. X-ray diffraction analysis and optical microscopy were used to study the crystalline structure of selected irradiated pigments in order to identify the changes that take place upon laser irradiation. Two representative pigments were studied, cinnabar (HgS) and lead white (Pb(OH)2 2PbCO3). The results revealed a change in the crystalline phase or chemical composition, respectively, which can be barely detected owing to its superficial character, which is of a sub-micrometer scale.