Biodiesel is a renewable, alternative diesel fuel of domestic origin derived from a variety of fats and oils by a transesterification reaction; thus, it consists of the alkyl esters, usually methyl esters, of the fatty acids of the parent oil or fat. An advantage of biodiesel is its potential to significantly reduce most regulated exhaust emissions, including particulate matter (PM), with the exception of nitrogen oxides (NOx). In this work, three fatty acid methyl esters, neat methyl laurate, neat methyl palmitate, and technical grade methyl oleate, were selected for exhaust emissions testing in a heavy-duty 2003 six-cylinder 14 L diesel engine with exhaust gas recirculation. These fuels were compared with neat dodecane and hexadecane as well as commercial samples of biodiesel and low-sulfur petrodiesel as the base fuel, thus establishing for the first time a baseline of the exhaust emissions of neat hydrocarbon (alkane) fuels versus neat methyl esters. All fuels were tested over the heavy-duty diesel transient cycle. PM emissions were significantly reduced with biodiesel and methyl oleate (about 77 and 73%, respectively), while reductions with methyl palmitate and methyl laurate were even greater (82-83%) compared to the petrodiesel fuel. PM emissions with biodiesel only slightly exceeded the upcoming emissions standards, raising the possibility that biodiesel may meet these standards using only a diesel oxidation catalyst without employing a particulate trap. NO, emissions increased with biodiesel (about 12%) and technical grade methyl oleate (about 6%) but decreased (about 4-5%) with methyl palmitate and methyl laurate relative to those of the base fuel. PM emissions decreased (about 45-50%) with both dodecane and hexadecane. NOx emissions were reduced (around 15.5-16%) with dodecane and hexadecane compared to those of the petrodiesel fuel. The methyl ester moiety influences exhaust emissions by reducing particulate matter considerably more than neat straight-chain hydrocarbons, which are enriched in "clean" petrodiesel fuels, while NOx exhaust emissions, which showed little chain-length dependence, are less reduced. Thus, no future "clean" petrodiesel fuel should be able to achieve the low PM exhaust emissions levels of biodiesel without additional additive treatments or support by engine technology. Unsaturated fatty esters show slightly increased NOx and PM emissions compared to their saturated counterparts. The soluble organic fraction of the PM emissions was higher for the ester fuels. Hydrocarbon (HC) and CO exhaust emissions were also determined. Although HC emissions were low, a strong effect of chain length was observed.