The Vienna Basin is situated at the contact of the Bohemian Massif, Western Carpathians, and Eastern Alps. Deep borehole data and an existing magnetotelluric profile were used in density modelling of the pre-Neogene basement in the Slovak part of the Vienna Basin. Density modelling was carried out along a profile oriented in a NW–SE direction, across the expected contacts of the main geological structures. From bottom to top, four structural floors have been defined. Bohemian Massif crystalline basement with the autochthonous Mesozoic sedimentary cover sequence. The accretionary sedimentary wedge of the Flysch Belt above the Bohemian Massif rocks sequences. The Mesozoic sediments considered to be part of the Carpathian Klippen Belt together with Mesozoic cover nappes of Alpine and Carpathian provenance are thrust over the Flysch Belt creating the third structural floor. The Neogene sediments form the highest structural floor overlying tectonic contacts of the Flysch sediments and Klippen Belt as well as the Klippen Belt and the Alpine/Carpathians nappe structures.