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In this paper, a polynomial controller based on the flatness property is designed for a diesel engine equipped with a variable geometry turbocharger (VGT) and an exhaust gas recirculation (EGR) valve. These two components have widely contributed to reduce the pollutant emission and to improve engine performance. For the control design, a simplified nonlinear model of the diesel engine is considered. This model is linearized around an operating point to design a linear polynomial controller based on the flatness property. The diesel engine variables are completely determined by the planning of the flat output trajectory in a discrete-time framework. The resulting controller is then applied on the nonlinear model initially considered. Simulations results on a real-time electronic test bed show the performance improvement in terms of tracking and robustness.