Disturbance of ecosystems is a major factor in regional carbon budgets, and it is believed to be partly responsible for the large inter-annual variability of the terrestrial part of the carbon balance. Forest fires have so far been considered as the most important disturbance but also other forms of disturbance such as insect outbreaks or wind-throw might contribute significantly to the largely unexplained inter-annual variability, at least in specific regions. The effect of wind-throw has not yet been estimated because of lack of data on how carbon fluxes are affected. The Gudrun storm, which hit Sweden in January 2005, resulted in ca. 66 million m3 of wind-thrown stem wood on an area of ca. 272 000 ha. Using a model (BIOME-BGC) calibrated to CO2 flux measurements at two sites, the annual net ecosystem productivity during the first year after the storm was estimated to be in the range −897 to −1259 g C m−2 yr−1. This is a much higher loss compared with harvested (clear-cut) forests in Europe, which ranged between ca. −420 and −100 g m−2 yr−1. The reduction in the carbon sink scaled to the whole wind-thrown area was estimated at ca. 3 million tons C during the first year. By historical data on wind-throw in Europe combined with modelling, we estimated that the large Lothar storm in 1999 reduced the European carbon balance by ca. 16 million tons C, this is ca. 30% of the net biome production in Europe. We conclude that the impact of increased forest damage by more frequent storms in future climate change scenarios must be considered and that intermittent large wind-throw events may explain a part of the large inter-annual variability in the terrestrial carbon sink.