Numerous Life Cycle Impact Assessment (LCIA) tools exist, each with different methodologies. These tools often provide different results, thus making it difficult for the LCA practitioner to determine which results yield the best or most likely estimate of impact. It is important, therefore, to understand the differences between LCIA tools to enable the clear and transparent portrayal of the impacts of a life cycle inventory. Differences among LCIA tools are compared by applying three impact assessment tools: IMPACT 2002+, TRACI, and CML to the life cycle inventory data for corn-soybean agricultural systems utilized to produce biofuels in the US. The agricultural system has grown in importance in the US as the primary source of feedstock materials for biobased production. The sources of differences between characterization factors and thus the impact assessment results are not readily apparent to the average user of these tools. For example, chemical contribution to the effects on human health and photochemical oxidation, in particular, vary considerably among the tools compared due to fundamentally different methodologies for impact estimation. Other impacts especially relevant to US agriculture are also discussed, including eutrophication and ecotoxicity. Suggestions for improvements to the impact assessment models are made, such as drawing a distinction between urban and non-urban emissions as well as inclusion of heavy metal speciation. Understanding why impact assessment tools provide different results can help agricultural and biobased LCA practitioners to choose the appropriate tool for their inventory.