The Menderes Massif is a major Alpide metamorphic complex in western Turkey; it is subdivided into southern, central, and northern submassifs by the east-west trending grabens. The basement of the southern Menderes Massif consists of Neoproterozoic micaschists (Selimiye Formation) intruded by Neoproterozoic granites. The basement is overlain by Permo-Carboniferous phyllite, marble, and quartzite (Goktepe Formation), which pass up into a thick sequence of Mesozoic marbles with emery horizons (Milas Marble). The marbles are overlain by latest Cretaceous recrystallized pelagic limestone and Paleocene metaclastics, which are thrusted over by the Lycian nappes. The metamorphism and deformation of the Phanerozoic sequence of the Menderes Massif is Eocene in age. The structure of the central Menderes Massif is controversial with views ranging from an inverted metamorphic sequence to a pile of nappes. Here we report the results from four deep (>3 km) geothermal wells from the central Menderes Massif. Two distinctive lithological units are differentiated in the wells. The top 0.5 to 1 km of the well sections are made up of micaschists, correlated with the Neoproterozoic Selimiye Formation, whereas the lower parts of the wells have cut through graphite-bearing quartzite, phyllite, and marble regarded as being parts of the Goktepe Formation and Milas Marble. The lithological differences are also picked up by a magnetotelluric study, which shows a sharp increase in the conductivity at the contacts of the Selimiye and Goktepe Formations. The question of whether the inversion of the stratigraphic sequence is due to thrusting or recumbent folding is still open.