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In order to study the spatial and temporal variations of the emissions of greenhouse gases and of their precursors, we developed a data assimilation system and applied it to infer emissions of CH₄, CO and H₂ for one year. It is based on an atmospheric chemical transport model and on a simplified scheme for the oxidation chain of hydrocarbons, including methane, formaldehyde, carbon monoxide and molecular hydrogen together with methyl chloroform. The methodology is exposed and a first attempt at evaluating the inverted fluxes is made. Inversions of the emission fluxes of CO, CH₄ and H₂ and concentrations of HCHO and OH were performed for the year 2004, using surface concentration measurements of CO, CH₄, H₂ and CH₃CCl₃ as constraints. Independent data from ship and aircraft measurements and satellite retrievals are used to evaluate the results. The total emitted mass of CO is 30% higher after the inversion, due to increased fluxes by up to 35% in the Northern Hemisphere. The spatial distribution of emissions of CH₄ is modified by a decrease of fluxes in boreal areas up to 60%. The comparison between mono- and multi-species inversions shows that the results are close at a global scale but may significantly differ at a regional scale because of the interactions between the various tracers during the inversion.