We present high-resolution Vp models of the Middle Aterno basin obtained by multi-scale non-linear controlled-source tomography. Seismic data have been collected along four dense wide-aperture profiles, that run SW-NE for a total length of ∼6 km in the hanging-wall of the Paganica-S. Demetrio Fault, source of the 6th April 2009 (Mw 6.3) L’Aquila normal-faulting earthquake. Seismic tomography expands the knowledge of the basin with high spatial resolution and depth penetration (>300 m), illuminating the Meso-Cenozoic substratum that corresponds to high-Vp regions (Vp>3500–4000 m/s). Low Vp (1500–2000 m/s) lacustrine sediments (Early Pleistocene in age) are imaged only in the SW sector of the basin, where they are up to 200 m thick and lie below coarse fluvial and alluvial fan deposits. The overall infill consists of Early Pleistocene to Holocene alluvial fan and fluvial sediments between the Paganica Fault and the Bazzano ridge, with Vp reaching 3000 m/s for the oldest conglomeratic bodies. The substratum has an articulated topography. The main depocenter, ∼350 m deep, is in the SW sector of the basin south of the Bazzano ridge. Remarkably, this depocenter and the overlying thick lacustrine body match the area of maximum coseismic subsidence observed after the 2009 earthquake. In the Paganica area, Vp images unravel large steps in the substratum related to two unreported SW-dipping buried strands, synthetic to the Paganica Fault, with ∼250 m associated total vertical throw. This finding has important implications on the long-term history of the Paganica-S. Demetrio Fault system, whose total vertical displacement has been previously underestimated. An additional ∼250 m vertical offset along this complex Quaternary extensional structure should therefore be considered.