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In our aim to decrease the consumption of materials and energy and promote the use of renewable resources, such as biofuels, rises the need to measure materials and energy fluxes. This paper suggests the use of Exergy Flow Analysis (ExFA) as an environmental assessment tool to account wastes and emissions, determine the exergetic efficiency, compare substitutes and other types of energy sources: all useful in defining environmental and economical policies for resource use. In order to illustrate how ExFA is used, it is applied to the process of biodiesel production. The results show that the production process has a low exergy loss (492MJ). The exergy loss is reduced by using potassium hydroxide and sulphuric acid as process catalysts and it can be further minimised by improving the quality of the used cooking oil.