A regional variational inverse modeling system for the estimation of European biogenic CO2 fluxes is presented. This system is based on a 50 km horizontal resolution configuration of a mesoscale atmospheric transport model and on the adjoint of its tracer transport code. It exploits hourly CO2 in situ data from 15 CarboEurope-Integrated Project stations. Particular attention in the inversion setup is paid to characterizing the transport model error and to selecting the observations to be assimilated as a function of this error. Comparisons between simulations and data of CO2 and 222Rn concentrations indicate that the model errors should have a standard deviation which is less than 7 ppm when simulating the hourly variability of CO2 at low altitude during the afternoon and evening or at high altitude at night. Synthetic data are used to estimate the uncertainty reduction for the fluxes using this inverse modeling system. The improvement brought by the inversion to the prior estimate of the fluxes for both the mean diurnal cycle and the monthly to synoptic variability in the fluxes and associated mixing ratios are checked against independent atmospheric data and eddy covariance flux measurements. Inverse modeling is conducted for summers 2002–2007 which should reduce the uncertainty in the biogenic fluxes by ∼60% during this period. The trend in the mean flux corrections between June and September is to increase the uptake of CO2 by ∼12 gCm−2. Corrections at higher resolution are also diagnosed that reveal some limitations of the underlying prior model of the terrestrial biosphere.