The Upper Jurassic ‘Malm’ carbonates of southern Germany are currently the most developed reservoir for geothermal energy production in Germany. Although many studies have investigated the Malm carbonate reservoir, few studies have focused on the palaeokarst system – despite the fact that the reservoir is frequently referred to as ‘Malmkarst’. Data from 25 wells in the Malm reservoir, including well logs, seismic data and hydraulic information, systematically demonstrate the presence of karstification. This is apparent in the form of large sinkholes and amplitude anomalies on the seismic scale, as well as caves observed in the image log and caliper log data. Flowmeter logs correlated with the karstified section on the image log reveal thin zones of elevated permeability, contributing most of the flow at the wellbore scale. The comparison between measurements from core data and well tests provides evidence of the reservoir's excess permeability, exhibiting values several orders of magnitude higher than those measurable in cores. The stratigraphic record suggests that karstification occurred during the Jurassic and Cretaceous, prior to the burial of the carbonates by the sediments of the alpine molasse basin.