Abstract To analyze the first-order structural features characterizing the crust and the lithospheric mantle below the Central European Basin System and adjacent areas, a new lithosphere-scale 3D structural/density model has been derived that integrates published knowledge with 3D gravity modeling. With this study we aim to integrate previous results on sub-domains of the study area and regional results of limited resolution in conjunction with 3D gravity analysis to derive the configuration of the lower crust and lithospheric mantle that is consistent with the known density distribution of the sediment fill and with observed deep seismic data as well as with observed gravity. The derived 3D density model resolves the internal configuration of the crystalline crust below the Central European Basin System and adjacent areas at the regional scale and shows that the crystalline crust is characterized by a layered structure. The upper to middle crystalline crust is characterized by relatively low seismic p-wave velocities and densities. It shows strong variations in thickness across the study area that partly correlate spatially with the inherited segmentation in response to crustal amalgamation. This upper to middle crystalline crust is underlain by a continuous high-density/high-velocity lower crustal layer, locally more than 30 km thick beneath the East European Craton and generally decreasing in thickness from the older to the younger tectonic domains. Though the thickness of this high-density lower crust is generally small below the Permo-Cenozoic Central European Basin System, it can reach locally more than 18 km below the Northeast German and the Norwegian–Danish basins. The derived depth to the lithosphere–asthenosphere boundary confirms previously proposed geometries and is up to 230 km deep beneath the Precambrian domain, but less than 100 km deep beneath the Phanerozoic domains, implying that the average thermal gradient is higher in the Phanerozoic lithosphere than in the Precambrian part.