Thirty apatite fission track ages and 22 track length measurements are presented from samples of basement rocks flanking the Malawi and Rukwa Rifts (East African Rift System) in order to elucidate the thermotectonic history of the rift flanks. The apatite fission track ages fall in the range 30 ± 15 to 296 ± 10 Ma. The relatively short (11.0-13.2 μm) mean track lengths and wide (1.3-2.3 μm) track length distributions suggest a protracted cooling history for the region, spanning Permian (Karoo) to Recent times. Thermal history reconstruction by inverse model calculations of the track length distribution suggests repreated phases of rapid cooling and denudation of the rift flanks at 150-200 Ma, ~150 Ma and ≤ 40-50 Ma. These appear to be linked to the different rifting events in the area and can be correlated with deposition of the different sedimentary units within the basins. Erosion and isostatic rebound have modified the tectonically induced topography around the rifts: the evevation of the footwall flanks is augmented by flexural isostatic rebound, whereas the topography of the hanging wall flanks has been lowered by erosion. The footwall escarpments of the Malawi and Rukwa rifts are erosional features. The highly elevated plateaus flanking the Western Rift represent an erosional surface traditionally referred to as the 'Gondwana surface'. The apatite fission track results of this study suggest that initial exhumation of the 'Gondwana surface' to temperatures around 60-70°C took place during Karoo times, but the sub-aerial exposure of the surface did not take place until at least the Early Tertiary.