The Maltese graben system is a series of Miocene–Quaternary extensional basins located in the foreland of the Sicilian Apennine–Maghrebian fold and thrust belt. The tectono-sedimentary development of the graben was determined from the first fully integrated analysis of the area to include onshore field and hydrological borehole data, together with offshore reflection seismic data and exploration wells. The NW–SE- and ENE–WSW-trending rifts have a coeval, four phase tectono-sedimentary evolution revealed by a succession of platform and pelagic carbonates. The pre-rift phase (>21 Ma) is followed by a early syn-rift phase (21–6 Ma) characterized by evidence for relatively minor extensional faulting including the development of neptunian dykes. Major fault activity occurred during the succeeding late syn-rift phase (<5 Ma) which is characterized by growth faults and fault control on facies and the areas of deposition/non-deposition. This was followed by passive graben infilling during the post-rift phase (probably < 1.5 Ma). Despite low measured extension factors (β = 1.03–1.17) across the rift structures, major basin bounding extensional faults have throws of up to 2.2 km. Fault slip data indicate that both NW–SE and ENE–WSW rift trends were generated in response to N–S stretching. These results are in accord with Argnanis (1990) description of a major N–S orientated transfer fault located 50 km west of the present study area.