The northern Fossa Magna (NFM) basin is a Miocene rift system produced in the final stages of the opening of the Sea of Japan. It divides the major structure of Japan into two regions, with north-trending geological structures to the NE of the basin and EW trending structures to the west of the basin. The Itoigawa-Shizuoka Tectonic Line (ISTL) bounds the western part of the northern Fossa Magna and forms an active fault system that displays one of the largest slip rates (4-9 mm/year) in the Japanese islands. Deep seismic reflection and refraction/wide-angle reflection profiling were undertaken in 2002 across the northern part of ISTL in order to delineate structures in the crust, and the deep geometry of the active fault systems. The seismic images are interpreted based on the pattern of reflectors, the surface geology and velocities derived from refraction analysis. The 68-km-long seismic section suggests that the Miocene NFM basin was formed by an east dipping normal fault with a shallow flat segment to 6 km depth and a deeper ramp penetrating to 15 km depth. This low-angle normal fault originated as a comparatively shallow brittle/ductile detachment in a high thermal regime present in the Miocene. The NFM basin was filled by a thick (>6 km) accumulation of sediments. Shortening since the late Neogene is accommodated along NS to NE-SE trending thrust faults that previously accommodated extension and produce fault-related folds on their hanging wall. Based on our balanced geologic cross-section, the total amount of Miocene extension is ca. 42 km and the total amount of late Neogene to Quaternary shortening is ca. 23 km. © 2004 Elsevier B.V. All rights reserved.