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Engine performance and emission comparisons were made between the use of 100% soy, Canola and yellow grease derived biodiesel fuels and an ultra-low sulphur diesel fuel in the oxygen deficient regions, i.e. full or high load engine operations. Exhaust gas recirculation (EGR) was extensively applied to initiate low temperature combustion. An intake throttling valve was implemented to increase the differential pressure between the intake and exhaust in order to increase and enhance the EGR. The intake temperature, pressure, and EGR levels were modulated to improve the engine fuel efficiency and exhaust emissions. Furthermore, a preliminary ignition delay correlation under the influence of EGR was developed. Preliminary low temperature combustion modelling of the biodiesel and diesel fuels was also conducted. The research intends to achieve simultaneous reductions of nitrogen oxides and soot emissions in modern production diesel engines when biodiesel is applied.