This work is about the influence of the molecular structure of the fatty acid esters present in two neat biodiesel fuels and their blend (50% by volume) on particulate matter emission. Experiments were performed in a four-cylinder direct injection automotive diesel engine under carefully controlled operating conditions, so that the difference in performance and emissions were affected only by biodiesel fuels composition and properties. The results indicated that the composition and degree of unsaturation of the methyl ester present in biodiesel plays an important role in the chemical composition of particulate matter (PM) emitted. It was observed that linseed biodiesel (BL100) produces more PM and hydrocarbons (HC) than Palm biodiesel (BP100) as a consequence of more unsaturated compounds in its composition, which favor the soot precursor's formation in the combustion zone. Thermogravimetric analysis (TGA) showed that the amount of volatile material in the soot from biodiesel fuels was slightly lower than that of diesel fuel, but not significant differences were observed among biodiesels. Similarly, the chemical characteristics of the hydrocarbons of volatile material present in the particulate matter (referred in the literature as SOF-soluble organic fraction), showed an increase in the aliphatic component as the unsaturation degree of the fatty acid methyl ester increased. Additionally, it is concluded that there are not significant nano-structural differences in the soot obtained from pure biodiesel fuels, even if they have very different degrees of unsaturation. (C) 2011 The Combustion Institute. Published by Elsevier Inc. All rights reserved.