This paper reports a three-dimensional numerical study, using the KIVA-3V code with modified chemical and physical models, of the exhaust (NOx and soot) emissions from an in-line, four-cylinder, 3.0 l, turbo-charged, direct injection diesel engine operated in spray diffusion combustion mode, by injecting fuel at top dead centre, in typical operating conditions for city driving (70 per cent load, 1500 r/min engine speed) with various exhaust gas recirculation (EGR) rates. To predict soot emission parameters, a gas-phase polycyclic aromatic hydrocarbons (PAH) precursor formation model was coupled with a detailed phenomenological particle formation model, including soot nucleation from the precursors, surface growth/oxidation, and particle coagulation, since changes in the surface area of particles and surface reaction rates had to be taken into account. In order to predict NOx emission parameters, the extended Zeldovich (thermal), intermediate N2O and NO2 from NO formation mechanisms were also included in the modelled elementary reactions. From the numerical simulation results, it was shown that the present code had sufficient performance for predicting the amount of exhaust soot and NOx with practical central processing unit (CPU) time. Comparison of the results of the numerical simulations with data obtained from empirical tests show that the applied code provides adequate predictions of soot and NOx emissions for engine design and optimization within practical CPU times. The results also show that the EGR rate does not greatly affect the soot surface growth rate, although it was previously thought to be a major determinant of soot masses. Instead, soot oxidation rates, especially rates of oxidation by OH radicals, were found to be the most influential factors affecting soot emissions under the tested engine operating conditions.