Biofuels have been proposed as an ecologically benign alternative to fossil fuels. There is, however, considerable uncertainty in the scientific literature about their ecological benefit. Here, we review studies that apply life-cycle analysis (LCA), a computational tool for assessing the efficiency and greenhouse gas (GHG) impact of energy systems, to biofuel feedstocks. Published values for energy efficiency and GHG differ significantly even for an individual species, and we identify three major sources of variation in these LCA results. By providing new information on biogeochemistry and plant physiology, ecologists and plant scientists can increase the accuracy of LCA for biofuel production systems.