The fatty acid alkyl esters derived from plants, rendered fats/oils and waste restaurant greases, commonly known as biodiesel, are renewable alternative fuels that may fulfill the demand gap caused by the depleting fossil diesel fuels. The combustion and emission characteristics of neat biodiesel fuels were investigated on a single cylinder of a 4-cylinder Ford common-rail direct injection diesel engine, which cylinder has been configured to have independent exhaust gas recirculation (EGR), boost and back pressures and exhaust gas sampling. The fatty acid methyl esters derived from Canola oil, soybean oil, tallow and yellow grease were first blended. Biodiesel engine tests were then conducted under the independent control of the fuel injection, EGR, boost and back pressure to achieve the low temperature combustion mode. Multi-pulse early-injections were employed to modulate the homogeneity history of the cylinder charge. Because of the high Cetane number of the biodiesel fuels used, the EGR was necessary to withhold the mixture from premature auto-ignition thus moderating the combustion phasing of the early-injection biodiesel low temperature combustion. This research intends to achieve in-cylinder simultaneous reduction of NOx and soot formation in modern production diesel engines when biodiesel is applied.