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In modern Diesel engines Exhaust Gas Recirculation (EGR) and Variable Geometry Turbochargers (VGT) have been introduced to meet the new emission requirements. A control structure that coordinates and handles emission limits and low fuel consumption has been developed. This controller has a set of PID controllers with parameters that need to be tuned. To be able to achieve good performance, an optimization based tuning method is developed and tested. In the optimization the control objectives are captured by a cost function. To aid the tuning a systematic method has been developed for selecting representative and significant transients that excite different modes in the controller. The performance is evaluated on the European Transient Cycle. It is demonstrated how weighting factors in the cost function influence control behavior, and that the proposed tuning method gives a significant improvement in control performance compared to standardized tuning methods for PID controllers.