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In order to make efficient use of a Diesel engine equipped with an SCR system, it's important to have a complete system approach when it comes to calibration of the engine and the aftertreatment system. This paper presents a complete model of a heavy duty diesel engine equipped with a vanadia based SCR system. The diesel engine uses common rail fuel injection, a variable geometry turbocharger (VGT) and cooled EGR. The engine model consists of a quasi steady gas exchange model combined with a two-zone zero dimensional combustion model. The combustion model is a predictive heat release model. Using the calculated zone temperatures, the corresponding NOx concentration is given by the original Zeldovich mechanism. The SCR catalyst model is of the state space type. The basic model structure is a series of continuously stirred tank reactors and the catalyst walls are discretized to describe mass transport inside the porous structure.