The Carbon Use Efficiency (CUE) is the ratio of net primary production (NPP) to gross primary production (GPP) and shows the capacity of terrestrial ecosystems to transfer carbon from the atmosphere to biomass. After 2000 there were four anomalous years in the productivity of terrestrial ecosystems caused by extreme droughts and heat waves in Southeast Europe in 2000, 2003, 2007 and 2012. The aim of this study is to examine the CUE under the stress conditions using NPP/GPP data products from the MODIS (NASA) spectroradiometer. Under extreme weather conditions CUE varied between 0.44 and 0.49, i.e. the drought and heat waves reduced the CUE with 10 до 20% and as a result the region has shifted from a carbon sink to a carbon source. Lowest CUE was observed in 2007, when it was 20% lower than efficiency in a normal year. The stress affects most on forest biomes, which were the lowest effective. It was found that up to 1100 m.a.s.l. the CUE decreased linearly with elevation, because of the predominant deciduous broadleaf forests.