This paper presents an improved sequence stratigraphic framework for the southern and central Vienna Basin (Austria) based on the integration of 3D seismic reflection data, well data, surface outcrops and refined biostratigraphy. The 3D survey used for this study is positioned close to the margin of the Vienna Basin, which increases the stratigraphic importance of this analysis. Distal basin facies, so far only known from seismic and well data, are compared and correlated to their proximal equivalents in surface outcrops. The investigated part of the basin is characterized by a syn-sedimentary horst and graben structure, with Badenian (Langhian and Lower Serravallian) platform carbonates on the elevated areas and fine-grained marine clastic sediments in adjacent subbasins. This integrated approach allows the separation of the Neogene sediments in the southern Vienna Basin into five Middle and Upper Miocene 3^rd order depositional cycles: the Badenian is separated into three depositional cycles and the Sarmatian (Middle and Upper Serravallian) and the Pannonian (Tortonian) represent one depositional cycle each. The three Badenian cycles are correlated with the TB 2.3., TB 2.4. and TB 2.5. cycles from global sea-level charts. A major sea-level drop of 90–120 m can be calculated for the boundary between TB 2.3. and TB 2.4. at roughly 14.2 Ma. The Sarmatian cycle corresponds to the TB 2.6. cycle and the Pannonian to the TB 3.1. cycle. Since these sequence boundaries are dated in other European basins, their correlation to the Vienna Basin provides improved time constraints for the stratigraphic evolution of the Vienna Basin. The results from this study in the southern Vienna Basin can be extrapolated to the central and probably also to the northern parts of the basin.