This paper describes a detailed analysis of the unsteady flows in the intake and exhaust systems of a modern four-cylinder, turbocharged Diesel engine by means of advanced numerical tools and experimental measurements. In particular, a 1D-3D integrated fluid dynamic model, based on the GASDYN (1D) and Lib-ICE (3D) codes, has been developed and applied for the schematization of the geometrical domain and the prediction of the wave motion in the whole intake and the exhaust systems, including the air cleaner, the intercooler, the after-treatment devices and the silencers. Firstly, a detailed 1D simulation has been carried out to predict the pressure pulses, average pressures and temperatures in several cross-sections of the pipe systems for different speeds and loads, considering the complex geometry of the air filter, the intake manifold, the intercooler and the exhaust manifold. An extensive set of measured data has been used to validate the model and refine the 1D schematic for the simulation of both steady operating points and some transients. Secondly, an integrated 1D-3D simulation as been carried out, to represent the complex shape components by hybrid 1D-3D computational domains, in order to point out the flow field and the non-planar wave motion. The use of an initial coarse 3D grid for the intake manifold during the first cycles has been introduced, to speed-up the calculation and then switch to more refined grids during the last simulation cycles. Similarly, a 3D mesh of the exhaust manifold, integrated with 1D pipes, has allowed to capture some details of the wave motion and pressure pulses at the turbine inlet.