Landmark based geometric morphometrics was applied to the analysis of the cephalic scales of three phylogenetically related lacertid lizards (Podarcis raffonei, P. sicula, P. wagleriana) from some islands of the central Mediterranean area in order to assess the pattern of geographic variation and the phenetic relationships among and within the three species. Twenty nine homologous landmarks were recorded on the half configuration of the cephalic scales. To compare geometric and biometric patterns of variation and to evaluate any static allometry, seven biometric measurements were also recorded on the whole body. The three species significantly differ from each other in both shape and size of the skull. The shape of the Sopraocular and the Parietal scales appears to be highly diagnostic and species-specific. The analysis of intraspecific variation in shape of the cephalic scales indicates that P. sicula is the less variable species within the studied geographic area, whereas Podarcis raffonei is the most variable species both in size and shape. Podarcis raffonei is characterized by a divergent allometric pattern, likely related to the small population size and highly fragmented geographic range of the species.