The Bayesian framework of CO2 flux inversions permits estimates of the retrieved flux uncertainties. Here, the reliability of these theoretical estimates is studied through a comparison against the misfits between the inverted fluxes and independent measurements of the CO2 Net Ecosystem Exchange (NEE) made by the eddy covariance technique at local (few hectares) scale. Regional inversions at 0.5 resolution are applied for the western European domain where ∼ 50 eddy covariance sites are operated. These inversions are conducted for the period 2002-2007. They use a mesoscale atmospheric transport model, a prior estimate of the NEE from a terrestrial ecosystem model and rely on the variational assimilation of in situ continuous measurements of CO2 atmospheric mole fractions. Averaged over monthly periods and over the whole domain, the misfits are in good agreement with the theoretical uncertainties for prior and inverted NEE, and pass the chi-square test for the variance at the 30% and 5% significance levels respectively, despite the scale mismatch and the independence between the prior (respectively inverted) NEE and the flux measurements. The theoretical uncertainty reduction for the monthly NEE at the measurement sites is 53% while the inversion decreases the standard deviation of the misfits by 38%. These results build confidence in the NEE estimates at the European/monthly scales and in their theoretical uncertainty from the regional inverse modelling system. However, the uncertainties at the monthly (respectively annual) scale remain larger than the amplitude of the inter-annual variability of monthly (respectively annual) fluxes, so that this study does not engender confidence in the inter-annual variations. The uncertainties at the monthly scale are significantly smaller than the seasonal variations. The seasonal cycle of the inverted fluxes is thus reliable. In particular, the CO2 sink period over the European continent likely ends later than represented by the prior ecosystem model. © Author(s) 2013. CC Attribution 3.0 License.