The well-understood Neogene Pannonian Basin was superimposed on an earlier, mostly Cretaceous compressional realm. Based on the interpretation of subsurface data sets, such as academic and industry reflection seismic and well data, the Eoalpine units of the Eastern Alps can and should be correlated beneath the northwest Pannonian Basin with corresponding tectonic units of the Western Carpathians. Similarly, the Eoalpine folded belt beneath the southeast Pannonian Basin has a structural style very similar to that of the internal part of the Eastern and Southern Carpathians. The level of understanding of these folded belts subcropping at the base of the Pannonian Basin system is poor compared to those of the existing models of the classical folded belt of the Carpathians. This mismatch is primarily caused by the subsurface nature of the problem and the pronounced overprint by Neogene extensional tectonics.

In the Pannonian Basin, several well-established and a few emerging exploration plays can be outlined. The key elements of the most important plays include Neogene compactional anticlines; structures related to neotectonic inversion and tectonic reactivation; stratigraphic traps in the deepest part of Neogene subbasins; Paleogene sandstones in structural traps; Senonian–Triassic carbonates in complex structural traps; and Mesozoic reservoirs in the Eoalpine (Cretaceous) and Mesoalpine (Paleogene) folded belts. The future of hydrocarbon exploration in the Pannonian Basin is largely the function of better geophysical imaging and advanced geological understanding of what lies beneath the mature Neogene extensional basin.