The carbon footprint for organic and conventional crop farming systems was assessed in Kaunas district (Central Lithuania) using the Life Cycle Analysis (LCA). Data from field experiments were applied to define the effects of the organic and conventional crop farming systems. Both manure and mineral fertilizers were applied to the conventional and only manure in the organic rotations. The closed chamber method was employed to calculate carbon footprints of emitted and absorbed CO fluxes. The carbon flows in different agro-ecosystems were also analysed by the estimation of the biomass and leaf area index. The carbon footprints per hectare obtained for the organic farming systems were significantly lower than those obtained for the conventional ones. These results imply that the analysis of the whole crop rotation based on the LCA remains an important issue for analysis of the effects of farming. The introduction of ley and maize into the both organic (OF) and conventional farming (CF) systems resulted in the highest sank of C rates from the atmosphere that has been accumulated in highest net ecosystem production (NEP). The estimates of the carbon footprint indicate the capability of crops to sequester atmospheric carbon in biomass. Nonetheless, out of the crops considered, only ley featured the positive carbon balance and the lowest environmental impact due to the lowest CO emissions and LCA indices in both farming systems. The results imply that reasonable crop-mix within the crop rotation schemes may lead to reduction of CO emissions (i.e. their environmental impact) and mitigation of the climate change. However, the differences between the carbon footprint for the OF and CF agroecosystems were insignificant in general.