A quality analysis including footprint modelling has revealed spatial and temporal structures in the quality of Eddy Covariance measurements for two highland sites located on the Tibetan plateau. Fetch analysis has shown, that up to 1/3 of the measurements do not fulfill assumptions necessary for a physically correct data processing. Despite this fact, measurements of latent heat-, CO₂- and momentum flux in general fulfill the quality test criteria to an extend that the results can be regarded as suitable for fundamental research, whereby usually certain wind sectors have been found violating basic assumptions. Measurements of the sensible heat flux allow for the usage in continuously running measurement, while still few indications of the quality assessment can not be explained due to local topography, but indicate organized structures and lead to the hypothesis of mesoscale flow patterns in the boundary layer.