The seismicity of the geological complexes of the northern part of the Eastern Alps, the Western Carpathians and the Bohemian Massif is investigated by means of new seismic stations and a review of earthquake catalogues available. Eleven earthquake catalogues are evaluated and checked for multiple entries, fake earthquakes and mistakes. The final data set of earthquakes covers the time span from 1267 to 2004 and comprises 1968 earthquakes in total. The resulting epicentral map provides a very detailed idea of the seismicity of this region. An attempt at a seismo-tectonic interpretation of earthquakes based on the geological overview of the region is presented. Gravity and airborne magnetometry data in addition to seismic events are collected and cross-border maps are compiled and analysed in order to determine the spatial extent of these geological structures. The Linsser filtering technique is used to trace faults at two depth horizons — 4 and 8 km. Correlation between the epicentres of earthquakes and lineaments derived from gravity data is discussed for major historical earthquakes such as Neulengbach (1590) or Scheibbs (1867). This data set enables us to determine seismically active fault structures and to get an insight into the fault system interaction. The ability to assess the potentially seismically active vertical and horizontal extent of fault structures enables improved hazard assessments in future. The magnetometric map shows a belt of positive anomalies which reflects the presence of magnetized rocks between the Bohemian Massif and the Alpine-Carpathian zone.