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A 2003 heavy-duty diesel engine (2002 emissions level) was used to test a representative biodiesel fuel as well as the methyl esters of several different fatty acids. The fuel variables included degree of saturation, the oxygen content, and carbon chain length. In addition, two pure normal paraffins with the corresponding chain lengths of two of the methyl esters were also tested to determine the impact of chain length. The dependent variables were the NOx and the particulate emissions (PM). The results indicated that the primary fuel variable affecting the emissions is the oxygen content. The emissions results showed that the highest oxygen content test fuel had the lowest emissions of both NOx and PM. As compared to the baseline diesel fuel the NOx emissions were reduced by 5 percent and the PM emissions were reduced by 83 percent.