This study investigates the effect of biodiesel chemical structure on diesel engine combustion properties and exhaust emissions in mechanical injection engines, in view of future emissions reduction by tailoring the fatty acid profile or processing of bio-feedstock. To achieve this, the individual fatty acid methyl esters (FAMES) that make up biodiesel were investigated for combustion and emissions. Research included the effect of FAME molecular structure (saturation degree and chain length). Selected FAME fuels included neat methyl esters and blends with rapeseed oil methyl esters (RME). Several chemical and physical properties of the fatty acids methyl esters were chosen to obtain the most significant properties in terms of PM and NOx emissions in this type of engines. Each fuel was tested in a single cylinder mechanical direct injection (DI) diesel engine for combustion and exhaust emissions, with particular emphasis upon particulate matter (PM) emissions. Statistical prediction models showed a correlation between exhaust emissions and the most significant fuel properties ranging from 88% to 97%. NOx emissions were found to increase as chain length (with exception of C18:0) and the degree of unsaturation of fatty acid methyl esters increased. Total hydrocarbons (THCs), carbon monoxide (CO), volatile organic fraction (VOF) and soot emissions increases as the chain length of hydrocarbons increases. Soot produced by short chain length FAME is easier to oxidise than soot from long chain FAME. The recommendation is that shorter chain saturated FAME fuels would be preferable in a combined emissions context. (C) 2012 Elsevier Ltd. All rights reserved.