Abstract We conducted a palaeomagnetic study on the Cenozoic sedimentary sequences of the Nankai Trough, recovered by the Integrated Ocean Drilling Program Expedition 322 in SE Japan. Sedimentary sections of Late Miocene age from the two subduction input sites (sites C0011 and C0012) recorded a pattern of magnetic polarity reversals that correlates well with the known magnetic polarity time scale. The polarity of characteristic remanent magnetization could be identified throughout the majority of the recovered cores of the two sites, following removal of a low-stability drilling-induced remanence. Most of the observed magnetostratigraphy from the characteristic directions is in good agreement with that to be expected from the stratigraphic position of the sequence deduced from the biostratigraphic data. Palaeomagnetic data from both shipboard and shore-based studies indicate changes in the rate of sedimentation from 9.5 to 2.7 cm/kyr at about 11 Ma, suggesting that some fundamental palaeoenvironmental change in the Shikoku Basin and/or significant tectonic event may have occurred in Late Miocene.