Studies of vegetation history are important, as past vegetation distribution and development provide information on the development of the Earth’s climate, palaeoecological conditions, as well as on the migration and activity of early humans. For studying the vegetation history of SE-Estonia, modern case-study approach was used on three lakes of different nature and archaeological background: one at the top of the Haanja Heights (Lake Plaani), one on the slope of the Heights (Lake Verijärv) and one at the foot of the Heights (Lake Lasva), which were analyzed sedimentologically and palynologically. Sediments in Lake Lasva and Verijärv are laminated and provide a very precise time-scale, enabling comparison of pollen records from Lake Lasva with historical data. The vegetation dynamics in SE-Estonian uplands has several distinctive features compared with lowland regions of Estonia, such as the earlier arrival of Picea, Ulmus and Quercus, stable broad-leaved woods due to suitable habitats in the mosaic landscape and later human influence. From the Lake Verijärv sequence an evidence of a catastrophic forest fire was found.