The genetic background of the craniofacial development is a sensitive topic: in this context twin studies have had a relevant role as they allow to understand the effect of genes on the anatomical variability observed in the population. In particular, monozygotic twins (MZT) share the same DNA and allow to evaluate the genetic component of a specific morphology. In order to understand the similarities and differences on the facial morphology of MZT in different portions of the face, a thirdbased, superimposition approach was applied to the 3D facial scans of 10 couples of MZT. The experimental subjects were acquired through a stereophotogrammetric system, after the identification of a set of reference landmarks on their facial surfaces. The landmarks were used to segment facial areas of interest from the 3D reconstructions and to subdivide them into thirds, according to the territories of distribution of trigeminal branches for somatic sensitivity. The left and right upper, middle and lower facial thirds of each MZT couple were pairwise superimposed and the root mean square (RMS) point-to-point distances were automatically calculated. Data were statistically analysed through a two-way ANOVA, setting the level of significance at 5%. Post-hoc tests were performed with the necessary reductions in the degrees of freedom. Results revealed statistically significant differences among thirds (p < 0.05), while no differences were found for facial sides (p > 0.05) or for the third x side interaction (p > 0.05). Post hoc tests showed statistically significant differences between the upper and the lower facial thirds, and the middle and lower facial thirds (p < 0.05), with the middle and lower thirds being the more different between the couples. In conclusion, stereophotogrammetric techniques can be valid instruments to analyse the facial morphology of MZT. The acquisition procedure is easy to perform, fast and free from risk, being suitable to obtain multiple subsequent 3D reconstructions. These reconstructions can be superimposed and locally analysed in order to provide an anatomically-based, detailed description of the most similar and different facial areas, useful for the evaluation of the genetic components of a specific morphology.