Eastern Indonesia is the site of intense deformation related to convergence between Australia, Eurasia, the Pacific and the Philippine Sea Plate. Our analysis of the tectonic geomorphology, drainage patterns, exhumed faults and historical seismicity in this region has highlighted faults that have been active during the Quaternary (Pleistocene to present day), even if instrumental records suggest that some are presently inactive. Of the 27 largely onshore fault systems studied, 11 showed evidence of a maximal tectonic rate and a further five showed evidence of rapid tectonic activity. Three faults indicating a slow to minimal tectonic rate nonetheless showed indications of Quaternary activity and may simply have long interseismic periods. Although most studied fault systems are highly segmented, many are linked by narrow (<3 km) step-overs to form one or more long, quasi-continuous segment capable of producing M > 7.5 earthquakes. Sinistral shear across the soft-linked Yapen and Tarera–Aiduna faults and their continuation into the transpressive Seram fold–thrust belt represents perhaps the most active belt of deformation and hence the greatest seismic hazard in the region. However, the Palu–Koro Fault, which is long, straight and capable of generating super-shear ruptures, is considered to represent the greatest seismic risk of all the faults evaluated in this region in view of important strike-slip strands that appear to traverse the thick Quaternary basin-fill below Palu city.