Joint seismic tomography exploiting P and S wave arrivals conducted before the 2011 Offshore Tohoku earthquake reveals an area comparable to the faulting surface for the 2011 March 11 event with different properties from other areas along the shallow part of the subduction zone. The differences are revealed by using a measure R of the relative variations in shear wavespeed and bulk-sound speed. Within the faulting area there are patches on the subduction zone with slightly reduced S wavespeed, and thus negative R, that appear to separate portions of the rupture with very different character. On the down-dip side there is strong short-period radiation, whilst the largest slip occurs up-dip with most energy release at longer periods. Segmentation of the slip process can be imaged by back projection of seismograms from the US Array; the areas of greatest energy release at short periods lie down-dip from the negative R anomalies. The main seismic moment release from broad-band seismograms lies on the updip side of the same anomalies. The structural variations on the subduction zone thus separate two regions with fundamental differences in the rupture process, stronger long-period radiation up-dip and stronger short-period radiation down-dip. These variations are likely to reflect features brought into the subduction zone, which may have acted as asperities that allowed this event to build up 30–40 m of strain in the near trench zone, making it much bigger than expected. Thus minor changes in the character of the subducted plate can have a significant influence on the behaviour of a great earthquake.