Middle Miocene (Serravallian; upper Badenian–lower Sarmatian) strata recovered in 10 cored boreholes (83 samples) from Bad Deutsch-Altenburg, Vienna Basin, Austria, were analysed palynologically for the first time. The strata belong to the Rabensburg Formation of the Baden Group. The lateral distribution of the boreholes in reference to a Mesozoic ridge makes this area interesting for studying various aspects such as distribution of deposits, stratigraphy and palaeoenvironmental reconstruction. A diverse and well-preserved in situ dinoflagellate cyst association has been identified. Middle Miocene age-diagnostic species including Cannosphaeropsis passio, Cerebrocysta poulsenii, Habibacysta tectata, Labyrinthodinium truncatum, Operculodinium? borgerholtense and Unipontidinium aquaeductum are recorded. Their occurrences allow correlation with dinoflagellate cyst biozonations on a regional scale. Based on the identified dinoflagellate cysts and by correlation with calcareous nannoplankton and ostracods, from the same set of samples, a Serravallian age – corresponding to a late Badenian and early Sarmatian age (regional Paratethys stages) – is confirmed. Reworked (Cretaceous and Paleogene) dinoflagellate cyst assemblages, also well preserved, were recorded abundantly from boreholes HA 521 and HA 573 (south-west of the Mesozoic ridge). In accordance with ostracods, the Badenian–Sarmatian boundary can be traced in the upper part of borehole HA 66 based on an abrupt change in the dinoflagellate cyst assemblages. The upper Badenian strata were deposited in a coastal to inner shelf environment with terrigenous (siliceous sand and clay) and carbonate sediments. The recorded dinoflagellate cysts reflect marine, tropical to warm-temperate climatic conditions. The composition of the recorded dinoflagellate cyst assemblages is very close to that of the Middle Miocene assemblages of the Mediterranean, indicating water exchanges between the Central Paratethys and the Mediterranean during the late Badenian (early Serravallian).