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The Iberian Pyrite Belt (IPB) hosts world-class massive sulphide deposits, such as Neves-Corvo in Portugal and Rio Tinto in Spain. In Portugal, the Palaeozoic Volcanic-Sedimentary Complex (VSC) hosts these ore deposits, extending from the Grândola-Alcácer region to the Spanish border with a NW–SE to WNW–ESE trend. In the study area, between the Neves-Corvo mine region and Alcoutim (close to the Spanish border), the VSC outcrops only in a small horst near Alcoutim. Sparse exploration drill-hole data indicate that the depth to the top of the VSC varies from several 100 m to about 1 km beneath the Mértola Formation Flysch cover. Mapping of the VSC to the SE of Neves-Corvo mine is an important exploration goal and motivated the acquisition of six 2D seismic reflection profiles with a total length of approximately 82 km in order to map the hidden extension of the VSC. The data, providing information deeper than 10 km at some locations, were integrated in a 3D software environment along with potential-field, geological and drill-hole data to form a 3D structural framework model. Seismic data show strong reflections that represent several long Variscan thrust planes that smoothly dip to the NNE. Outcropping and previously unknown Late Variscan near-vertical faults were also mapped. Our data strongly suggest that the structural framework of Neves-Corvo extends south-eastwards to Alcoutim. Furthermore, the VSC top is located at depths that show the existence within the IPB of new areas with good potential to develop exploration projects envisaging the discovery of massive sulphide deposits of the Neves-Corvo type. © 2016, Springer-Verlag Berlin Heidelberg.