In Lithuania, the number of European pond turtles Emys orbicularis decreased between 1975 and 2010, but increased significantly between 2010 and 2014, when the LIFE project was implemented. During this project, an ecological network was created, habitats were restored in protected areas, and European pond turtle nesting areas were protected from predators. Very few morphometric measurements of European pond turtles are carried out in Lithuania. The purpose of this study was to perform morphometric measurements, assess migration, spread, and morphometric size variation. Morphometric measurements of juvenile European pond turtles showed that the morphometric indicators depended on the place of habitation: males from Juodabalė Zoological Reserve (Meteliai Regional Park) are smaller than females. Also, female turtles from Meteliai Regional Park are larger than both males and females from Kučiuliškė Herpetological Reserve. When comparing the morphometric indicators of males and females at ten months of age, sexual dimorphism is already observed: the shell height, the width of the head, carapace, and plastron of a females are already bigger than those of males.