The present study is the first attempt to carry out an inventory of greenhouse gas (GHG) fluxes in the forests of Estonia. The emission and uptake of CO2 as a result of forest management, forest conversion and abandonment of cultivated lands in Estonia was estimated. The removal of GHG by Estonian forests in 1990 exceeded the release about 3.3 times. Changes in the species composition and productivity of forest sites under various simulated climate change scenarios have been predicted by using the Forest Gap Model for the central and coastal areas of Estonia. The computational examples showed that the changes in forest community would be essential.