The hardware scatters as well as the engine parameters calibration have strong influences on exhaust emissions in recent diesel engines. In this research DoE(Design of Experiments) optimizations were done to study the possibility of minimizing the emission deviations caused by flow rate scatters of the injectors. It has been shown that the optimization of engine calibration, which minimizes the emission deviations, is feasible by establishing a target function representing the emission deviations for test results of maximum, mean and minimum flow rate injectors. It has also been shown that optimization of both emission deviations and emission level is possible by sequential DoE optimizations of the target functions representing the emission level and the emission deviations respectively with the appropriate boundary limits.