Biofuels are widely seen as substitutes for fossil fuels to offset the imminent decline of oil production and to mitigate the emergent increase in GHG emissions. This view is, however, based on too simple an analysis, focusing on only one piece in the whole mosaic of the complex biofuel techno-system, and such partial approaches may easily lead to ideological bias based on political preference. This study defines the whole biofuel techno-system at three scales, i.e., the foreground production (A), the background industrial network (B, including A), and the supporting Earth biosphere (C, including B). The thermodynamic concepts of energy, exergy and emergy measure various flows at these three scales, viz, primary resources, energy and materials products, and labor and services. Our approach resolves the confusion about scale and metric: direct energy demand and direct exergy demand apply at scale A; cumulative energy demand and cumulative exergy demand apply at scale B; and energy is applied at scale C, where it is named emergy, while exergy also can be applied at scale C. This last option was not examined in the present study. The environmental performance of the system was assessed using a number of sustainability indicators, including resource consumption, input renewability, physical benefit, and system efficiency, using ethanol from corn stover in the US as a technology case. Results were compared with available literature values for typical biofuel alternatives. We also investigated the influence of methodological choices on the outcomes, based on contribution analysis, as well as the sensitivity of the outcomes to emergy intensity. The results indicate that the techno-system is not only supported by commercial energy and materials products, but also substantially by solar radiation and the labor and services invested. The bioethanol techno-system contributes to the overall supply of energy/exergy resources, although in a less efficient way than the process by which the Earth system produces fossil fuels. Our results show that bioethanol cannot be simply regarded as a renewable energy resource. Furthermore, the method chosen for the thermodynamic analysis results in different outcomes in terms of ranking the contributions by various flows. Consequently, energy analysis, exergy analysis, and emergy analysis jointly provide comprehensive indications of the energy-related sustainability of the biofuel techno-system. This thermodynamic analysis can provide theoretical support for decision making on sustainability issues. (C) 2011 Elsevier Ltd. All rights reserved.