Oligocene trachytes from the Euganean Hills include various regionally metamorphosed gneissic and granulitic xenoliths. These xenoliths provide the unique opportunity to investigate Southalpine intermediate to deep crustal levels that are not presently exposed in the Eastern Alps. The estimated P-T conditions are in the range 780-850°C and 0.45-0.55 GPa for a migmatitic gneiss xenolith. The SHRIMP II U-Pb analyses on zircon from this xenolith provide concordant ages around 259.7±3.5 Ma, consistently with a PIXE U-Th-Pb age on monazite of 262±12 Ma. The Sr-Nd-Pb isotopic compositions, and major and trace element data show distinct origin for the different types of xenoliths. Mafic granulite xenoliths have an isotopic signature close to mantle-derived rocks and to Permian gabbroic rocks from the western-southern Alps. Metapelite xenoliths have high Sr and low Nd initial ratios like those of acid crustal rocks and could possibly represent the source of the crustal component, which is dominant in the acid Permian super-volcanoes. The migmatitic xenolith provides the first documented evidence for a Permian thermal event associated with crustal thinning in the Eastern Southern Alps. Here the Southalpine basement escaped most of the Alpine crustal shortening and still preserves most of the original Permian extension under thick Mesozoic covers.