Abstract The complicated structural and rheologic properties of Western Carpathian lithosphere reflect the complex geodynamic history of the Carpathian orogen. Based on critical analysis of earlier models, new interpolation of existing geophysical data and results of integrated modelling, a new map of the lithosphere thickness for the Carpathian–Pannonian region has been constructed. The map allows for the distinction of a frontal orogen collision zone in the NE (from increased lithosphere thickness) as well as a zone of oblique collision with the Bohemian Massif in the West, where lithosphere is not significantly thickened. The MOHO discontinuity beneath the Western Carpathian hinterland (Danube and East Slovak Basins), as defined by deep reflection seismic profiling, is relatively shallow. This probably reflects recent crustal extension related to oblique collision between the European plate and the ALCAPA block and an increase of the asthenospheric updoming from the Middle Miocene onward. Crustal thickness reflects the combined effects of deep-seated orogenic processes and mantle thermal evolution beneath the Pannonian Basin system. In this study, we focus particularly the structures of: (1) the Late Alpine collision and Neogene back arc basin development, including deep-seated contacts between colliding plates, a zone of slab detachment, the compressional accretionary wedge of the Outer Western Carpathian Flysch Belt, and extensional structures produced by subduction rollback and asthenosphere upwelling; (2) Early Alpine structures related to Cretaceous thrust-stacking, including subhorizontal reflection packages (interpreted as multi-generational extensional structures), the underplated intra-Penninic (Oravic) continental ribbon, and ophiolite traces of the Meliatic oceanic suture; and (3) north-dipping reflectors interpreted as remnant Hercynian lithotectonic fragments with opposed vergency to the subducted Alpine units.