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The exchange of carbon dioxide (CO2) between the atmosphere and a forest after disturbance by wind throw in the western Russian taiga was investigated between July and October 1998 using the eddy covariance technique. The research area was a regenerating forest (400 m × 1000 m), in which all trees of the preceding generation were uplifted during a storm in 1996. All deadwood had remained on site after the storm and had not been extracted for commercial purposes. Because of the heterogeneity of the terrain, several micrometeorological quality tests were applied. In addition to the eddy covariance measurements, carbon pools of decaying wood in a chronosequence of three different wind throw areas were analysed and the decay rate of coarse woody debris was derived. During daytime, the average CO2 uptake flux was −3 µmol m−2s−1, whereas during night‐time characterised by a well‐mixed atmosphere the rates of release were typically about 6 µmol m−2s−1. Suppression of turbulent fluxes was only observed under conditions with very low friction velocity (u* ≤ 0.08 ms−1). On average, 164 mmol CO2 m−2d−1 was released from the wind throw to the atmosphere, giving a total of 14.9 mol CO2 m−2 (180 g CO2 m−2) released during the 3‐month study period. The chronosequence of dead woody debris on three different wind throw areas suggested exponential decay with a decay coefficient of −0.04 yr−1. From the magnitude of the carbon pools and the decay rate, it is estimated that the decomposition of coarse woody debris accounted for about a third of the total ecosystem respiration at the measurement site. Hence, coarse woody debris had a long‐term influence on the net ecosystem exchange of this wind throw area. From the analysis performed in this work, a conclusion is drawn that it is necessary to include into flux networks the ecosystems that are subject to natural disturbances and that have been widely omitted into considerations of the global carbon budget. The half‐life time of about 17 years for deadwood in the wind throw suggests a fairly long storage of carbon in the ecosystem, and indicates a very different long‐term carbon budget for naturally disturbed vs. commercially managed forests.

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