Environmental pollution by metals and metalloids can have a detrimental effect on the fitness and development of organisms. Studies on the influence of metals and metalloids as environmental stressors on developmentally and functionally complex morphological structures of reptiles are important, as this group of vertebrates is highly threatened and is an important component of food webs. To assess the effects of chronic mercury exposure on cranium morphology and post-natal development in a model species of lizards, we analysed the concentration of this metal in liver tissues in the population of the Common wall lizard (Podarcis muralis) from the mercury mine tailings and the control population, and possible differences in skull size, shape, developmental stability and canalization between the two groups. Patterns of variation and asymmetry of the cranium shape were analysed using geometric morphometrics. The mercury concentration was significantly higher in the population from the polluted locality, but had very little to no effect on the cranial morphology. Juveniles and females from both sites had the same size and shape of the dorsal and ventral cranium, while males showed small differences in ventral cranium shape, reflected in slightly longer maxillae and wider crania at the polluted site. The pattern of sexual dimorphism remained constant at both localities. Both static and ontogenetic allometry were significant in both groups, and allometric trajectories did not differ between the two sites. The differences in fluctuating asymmetry (FA) between localities were not statistically significant for the dorsal and ventral cranium. The results do not support the idea that FA can be used as an early indicator mercury exposure at the population level.