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Effects of clear cutting and other forest disturbances on surface radiative properties and the energy and CO2 fluxes between land surface and the atmosphere can vary significantly depending on local climatic and moisture conditions, forest structure and species composition, soil properties and many other factors. In this study we analyzed the influence of clear-cutting on the energy, water vapor and CO2 fluxes in the still very poorly investigated part of the boreal forest community in the European part of Russia. This issue has become particularly relevant due to intensified logging in the region during recent decades. The sensible (H) and latent (LE) heat, as well as CO2 fluxes were continuously measured at recently clear-cut and undisturbed mature spruce forest sites using eddy covariance technique during the first growing season following harvest. Because of their close location they are characterized by similar meteorological conditions. The results of our field measurements showed that the clear-cut strongly influenced the energy balance and CO2 fluxes between the land surface and atmosphere. Energy fluxes (LE and H) at the undisturbed forest site were consistently larger than at the clear-cut throughout the period of measurements. The Bowen ratio (beta = H/LE) varied significantly over time, though was similar at both sites. Whereas H was almost equal to LE at both sites in spring, the LE significantly exceeded H over the summer (beta approximate to 0.2 - for mature spruce forest and beta = 0.4 - for clear-cut). The mean beta for the entire period was similar (beta approximate to 0.5) at both sites. Analysis of CO2 fluxes showed that the clear-cut was a consistent source of CO2 to the atmosphere. Net ecosystem exchange (NEE) at the clear-cut averaged 3.3 +/- 1.3 gC.m(-2).d(-1) (+/- 1 SD), while average NEE at the undisturbed mature forest was close to zero (0.1 +/- 1.9 gC.m(-2).d(-1)). Differences in NEE were mainly governed by differences in gross primary productivity (GPP) between sites (7.0 +/- 4.1 gC.m(-2).d(-1) and 4.1 +/- 3.0 gC.m(-2) .d(-1), for the undisturbed forest and clear-cut, respectively). Total ecosystem respiration (TER) did not significantly (p < 0.05) differ between sites (7.1 +/- 3.6 gC.m(-2).d(-1) at the undisturbed mature forest and 7.4 +/- 3.4 gC.m(-2).d(-1) at clear-cut). TER at the undisturbed forest showed higher sensitivity to changes in soil temperature, whereas GPP at the clear-cut was characterized by higher light-use efficiency. Our measurements showed that TER rates were relatively high in the southern taiga in comparison with other boreal sites where CO2 fluxes were previously investigated.