The processing and quality control of eddy covariance data during LITFASS-2003 experiment were discussed. A comprehensive turbulence software package TK2 was used for the data calculation and necessary corrections of the covariances, as well as the quality tests for the resulting turbulent fluxes. The application of the quality control procedure on the data from the micrometeorological allows to asses the quality of turbulent fluxes. The use of calculated surface soil heat flux also provide much better closure of the energy balance than using pure plates measurements.