Since 60 Myr, Peloponnesus and continental Greece have been affected by the Hellenidean compressional and the Aegean extensional phases. This complex evolution resulted in development of a strongly inhomogeneous crust in the Gulf of Corinth region. To study this area, we use a large strain thermomechanical numerical code PARAVOZ previously used for a number of similar problems such as rift evolution. Yet, instead of varying boundary and initial conditions applied to a plane-layered model, we use available geophysical constraints on the actual deep structure of the lithosphere to test its different possible initial structures. By varying the position of the initial crustal heterogeneity versus the position of the lithospheric slab, we are able to explain the origin of the internal structures and the kinematics of the Gulf of Corinth. The results suggest that the development of shear zones in the lower crust is favored by the gravitational collapse of the thicker part of the crust, whereas the geometry and the kinematics of these shear zones are controlled by the position of the edge of the slab. Asymmetry is seen in cases when a horizontal shift exists between the edge of the slab and the thicker part of the crust. Our model explains the differences between the northern shore and the southern shore as well as the east west variations observed in the Gulf of Corinth.