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For the first time, two-dimensional basin and petroleum systems modelling was performed along north-south cross sections in the Alpine Molasse Basin in Austria. The study has been performed with a special focus on the thrustbelt at the southern border of the basin which is very ambitious to model. Borehole information combined with 2D seismic interpretations built the data base for the reconstruction of the basin geometry. Temperature-sensitive parameters have been used to calibrate the thermal evolution of the basin. Prominent young uplift and erosion in the northeastern part of the Molasse basin was considered in the models and quantified using shale-compaction data derived from sonic logs. The best match between temperature, heat flow and observed maturities is reached for low heat flow values over time with a significant southward decreasing trend. Generation of hydrocarbons commenced during Miocene, coeval with the overthrusting nappe system of the Northern Calcareous Alps. Due to low heat flow values of 30 to 60 mW/m2, the oil kitchen is limited to the zone below the Alpine Nappes.