The Late Neogene and Quaternary sedimentary record within the Maltese islands is very fragmentary and has generally been ignored by sedimentologists. Local stratigraphies for parts of the Quaternary have been erected from vertebrate remains contained in Quaternary cave and fissure deposits of the islands. However, no coherent correlation scheme has been proposed in which to encompass them. The situation is exacerbated by the absence of datable fossils within the majority of Quaternary deposits. Considerable progress in resolving these problems is, however, possible if recourse is made to the post-Messinian (Late Miocene) erosion features evidenced in the topography of the islands. In particular, a hitherto unrecognized marine erosion surface, the San Leonardo Marine Abrasion Surface, is described and dated by reference to the marine deposits (San Leonardo Beds) lying directly above it and similarities to contemporaneous SE Sicily marine deposits. This provides an end-Calabrian Stage (Emilian Sub-Stage) base line upon which to hang fragmentary information on later events that have shaped the topography of the Maltese islands. From this it can be confirmed that a tectonic deformation event spanning latest Messinian to mid- Pliocene times uplifted the islands and reactivated previously incipient graben systems. This deformation episode is shown to have ceased within the islands well before the early Calabrian (before c. 1.6 Ma). Subsequent minor regional uplift and eustacy together with subaerial weathering processes have been the principal agents in shaping the islands. Collectively, these processes have prevented terrestrial animal migrations into the Maltese islands from North Africa since Messinian times. However, the infrequent re-establishment of a marine lowstand isthmus virtually linking Malta with SE Sicily has permitted opportunistic animal migrations into the islands and the presence of these greatly aids in dating the sedimentological events.