The South African government ratified a new biofuels industrial strategy at the end of 2007. The feasibility study that forms the basis of the strategy highlights the potential environmental implications of such a strategy. However, at present there is no structured approach to evaluate the environmental profile of the scenarios within the strategy. This paper introduces life cycle inventories whereby the environmental profiles of biofuel value chains may be evaluated meaningfully. The scope of the paper focuses on the seed extraction biodiesel production scenarios of the strategy. The inventory analysis shows that the inputs and outputs of the farming unit process are sensitive to the type of crop and region of produce. Water usage is a highly variable parameter, which emphasises the importance of rainfall and irrigation to the overall burden of the biodiesel system on water resources. Crop yields may differ by a factor of two, which is a significant difference in terms of land and non-renewable energy resources requirements. The oil and meal/cake content of the seed proves to be the most important parameter that influences the initial unit processes of the value chains; almost all the inputs and outputs of the farming unit processes, for all the crops, range in the order of a factor of two due to this parameter. The uncertainties associated with the logistic system in the value chain also have major implications. Further, should there be no market offset for the meal/cake co-products, the waste treatment requirements would be highly uncertain. Very little uncertainties were detected in the biodiesel production unit process, although the energy efficiency, and sustainability, of the overall production system remains questionable. The paper identifies a number of limitations with inventory sets that need to be addressed through further research efforts to improve the environmental evaluations of a biofuel value chain in South Africa for policy-making purposes.