The morphotectonic structure of the North Aegean Basin is studied on the basis of a new detailed swath bathymetric survey. The resulting bathymetric map is presented in reduction with 20-m isobaths. The slope analysis gives an accurate scheme of the geometry of the basin and distinction of several sub-basins (approximately 20). The overall basin geometry is a rectangular tetrahedron shaped by the major slope discontinuity separating the continental platform from the continental slope. The area distribution with depth shows a maximum at depths between 300 and 450 m along the sub-horizontal edge of the continental platform and at depths between 1000 and 1200 m at the basinal areas of the sub-basins. The separation of the western part of the North Aegean Basin from the eastern part (Saros Bay) is very clear in the area between Limnos and Thasos, with a maximum depth of 490 m. The 3.2% of the basin area is characterized by slope values >20%, which correspond to active fault zones. Their trend is NE-SW (N46o) and NW-SE (N136o). Some secondary E-W faults are also present within the basin with morphological expression only on the orientation of slopes <1%, reflecting deformation of the flat-lying deep parts of the basin’s interior. The overall geometry and inferred kinematics of the basin show an increase of both the vertical and horizontal components of the movement at the SW corner of the basin, where an opening of 40 km and a subsidence of 1600 m are contrasted to an opening of 20 km and a subsidence of 1000 m at the NE margin. The GPS data of the area showing an opening of 30 mm/yr are compatible with the above cumulative deformation for a neotectonic period of 4-5 Ma.