Due to increasingly strict emission regulations for IC engines, there is a significant motivation to investigate the relevant physical processes with the objective to reduce the reduction of exhaust gas emissions. Spray characteristics play a progressively important role in the consequent processes of mixture formation, ignition, combustion and pollutant formation in direct injection diesel engines. It is also important to develop an understanding of the atomization qualities of alternative fuels such as Biodiesel fuels as potential substitutions for conventional diesel fuel. In this research, the effect of injection and ambient parameters on spray breakup and atomization of different alternative fuels are investigated using CFD simulation. An Eulerian-Lagrangian approach is implemented in order to study the interaction of the continuous and discrete phases. Numerical simulations are extensively validated via experimental data available in literature for a constant volume chamber under ultra-high injection conditions up to 300 MPa. Simulated spray tip penetration, spray cone angle and spray images are compared with experiments and analytical correlations for three fuel types (diesel, palm oil, cooked oil), three injection pressures (100, 200, 300 MPa), and two ambient densities (15, 30 kg/m₃). Effect of mesh structure and two breakup models (WAVE and KHRT) on spray penetration were also investigated. Particle size distribution in radial and axial directions was studied.