Biomass is a renewable feedstock for producing modern energy carriers. However, the usage of biomass is accompanied by possible drawbacks, mainly due to limitation of land and water, and competition with food production. In this paper, the analysis concerns so-called second generation biofuels, like Fischer-Tropsch fuels or Substitute Natural Gas which are produced either from wood or from waste biomass. For these biofuels the most promising conversion case is the one which involves production of syngas from biomass gasification, followed by synthesis of biofuels. The thermodynamic efficiency of biofuels production is analyzed and compared using both the direct exergy analysis and the thermo-ecological cost. This analysis leads to the detection of exergy losses in various elements which forms the starting point to the improvement of conversion efficiency. The efficiency of biomass conversion to biofuels is also evaluated for the whole production chain, including biomass cultivation, transportation and conversion. The global effects of natural resources management are investigated using the thermo-ecological cost. The energy carriers' utilities such as electricity and heat are externally generated either from fossil fuels or from renewable biomass. In the former case the production of biofuels not always can be considered as a renewable energy source whereas in the latter case the production of biofuels leads always to the reduction of depletion of non-renewable resources. (C) 2013 Elsevier Ltd. All rights reserved.