Several research works have been carried out on biodiesel combustion, performance and emissions till today. But very few studies have been made about the chemistry of biodiesel that affects the diesel engine operation. Biodiesel is derived from vegetable oil or animal fats, which comprises of several fatty acids with different chain length and bonding. The present work focuses on the effect of biodiesel molecular weight, structure (Cis & Trans), and the number of double bonds on the diesel engine operation characteristics. Three types of biodiesel with different molecular weight and number of double bond were selected for the experimental studies. The biodiesels were prepared and analyzed for fuel properties according to the standards. A constant speed diesel engine, which develops 4.4 kW of power, was run with biodiesels and its performance was compared with diesel fuel. The results show that Linseed oil methyl ester with high linolenic (unsaturated fatty acid ester) does not suit best for diesel engine due to high oxides of nitrogen emission and low thermal efficiency. (C) 2010 Elsevier Ltd. All rights reserved.