Complying with emissions legislation presents ever increasing challenges for heavy duty diesel engines. These challenges are being met through the use of ever more sophisticated engine hardware. An example of such hardware is common rail fuel injection equipment which gives the flexibility of controlling fuel injection timing, pressure and quantity independently of engine speed and load. However, this greater flexibility increases the complexity of the engine optimisation process. The use of statistical experimental design, mathematical models and genetic algorithm techniques allows efficient and accurate quantification of the trade-offs needed to make sound engineering decisions during the optimisation process.