The Mura Depression is located at the SW border of the Pannonian Basin in the transition zone to the Eastern Alps. The Periadriatic Lineament, Labot, Ljutomer and Raba faults govern its structural characteristics. Ridges trending in the NEE–SWW direction divide the depression into three sub-basins. Therefore, the thickness of Miocene to Quaternary sediments varies considerably. The greatest depth to the Paleozoic metamorphic rocks is over 5500 m in the Ptuj-Ljutomer synform. The structure of the pre-Tertiary basement is well resolved by seismic reflection, gravity and magnetic investigations, as well as by drilling for hydrocarbons and thermal water exploration. The main tectonic units of the Mura Depression were correlated by using geophysical data to the structures outcropping at its western and southern rims. A compiled structural map of the pre-Tertiary basement is presented and geophysical and structural characteristics of main geotectonic units discussed. Beside minor production of oil and gas, the Mura Depression is an important geothermal area. Some locations were also explored as promising for the construction of an underground gas storage facility in aquifers.