We present 24 new apatite fission track (AFT) ages and 18 track length measurements from the Baikal region, SE Siberia. Most samples have AFT ages between 140 and 100 Ma, with relatively high mean track lengths (c. 13.2 μm). The relationship between AFT ages, elevation and mean track lengths indicate that the samples record rapid cooling during the Early Cretaceous (140–120 Ma), as also shown by thermal history inversion of track length distributions. Cooling took place during a Late Jurassic-Early Cretaceous orogenic phase, related to closure of the Mongol-Okhotsk ocean and reflected in the exhumation of metamorphic core complexes followed by thrusting and reverse faulting, basin inversion and large vertical motions. The variation in AFT ages throughout the study area can be partly explained by differences in geothermal structure but differential denudation also played a role. Minimum amounts of Early Cretaceous denudation are estimated at 2–3 km.