The present chapter presented two different examples for the design and analysis of modern CR equipped Diesel engines. A tool for multi-objective optimization was found very useful at the engine design stage to reduce the time-to-market of new engine prototypes, thanks to the possibility to effectively evaluate the influence of geometrical and operating engine parameters. In addition, a similar technique was applied to find the optimal selection of the control parameters (namely the injection strategy) in order to obtain an better engine behaviour. To reach the above objectives, different simulation techniques were employed, resorting to 1D, 3D and acoustic analyses. More accurate or simplified approaches were presented and differently used along the different phases of the engine development process. In each case, a continuous exchange of information among the various methods allowed to improve the overall simulation accuracy and results reliability. The whole procedure hence represents a very useful tool to reduce the huge experimental activity usually required to design and develop a modern CR diesel engine.