The effects of numerical methodology in defining the initial conditions and simulating the compression stroke in D.I. diesel engine CFD computations are studied. Lumped and pointwise approaches were adopted in assigning the initial conditions at IVC. The lumped approach was coupled with a two-dimensional calculation of the compression stroke. The pointwise methodology was based on the results of an unsteady calculation of the intake stroke performed by using the STAR-CD code in the realistic engine and port geometry. Full engine and 60 deg. sector meshes were used in the compression stroke calculations in order to check the accuracy of the commonly applied axi-symmetric fluid dynamics assumption. Analysis of the evolution of the main fluid dynamics parameters revealed that local conditions at the time of injection strongly depend on the numerical procedure adopted. Combustion computations, made with a modified version of the KIVA code, showed that differences in local temperature or equivalence ratio distribution play a key role in emission predictions even if their influence on the main combustion parameters is low.