Over the last decade, the interest in and production of biofuels has grown rapidly. Renewable transportation fuels can be produced from a variety of substrates, using various processing strategies. Feedstock preference and factory scale are geographic dependent. However, it is important to understand the implications of deploying these types of systems on a large scale, both throughout the U.S. as well as globally. To assess the sustainability of various biofuel options, it is crucial to evaluate their performance according to a number of attributes. This has been done using Life Cycle Assessment (LCA). Even so, comparisons among biofuel options are not easily accomplished. The objective of this study was to examine the efficiency of various biofuel options by using criteria which are important to LCA, namely, net energy balance and net carbon dioxide emission, and then compare them using Data Envelopment Analysis (DEA). Biofuel options examined included soy biodiesel, conventional corn ethanol, cellulosic ethanol (switchgrass, poplar, corn stover), and algae biofuel. This comparative approach is illustrated with a numerical example, which found that, using these criteria, soy biodiesel was most efficient. This study is a first step toward a more comprehensive assessment of biofuels, which will need to include additional criteria beyond those considered here. Each of these biofuels will need to be investigated for each criterion, not just from a production perspective, (i.e., quantity required and cost per unit), but also in terms of intangible criteria as well.