In this work an integration between a 1D code (Gasdyn) with a CFD code (OpenFOAM®) has been applied to improve the performance of a Moto3TM engine. The four-stroke, single cylinder S.I. engine was modeled, in order to predict the wave motion in the intake and exhaust systems and study how it affects the cylinder gas exchange process. The engine considered was characterized by having an air induction system with integrated filter cartridge, air-box and intake runner, resulting in a complex air-path form the intake mouth to the intake valves, which presents critical aspects when a 1D modeling is addressed. This paper presents a combined and integrated simulation, in which the intake systems was modeled as a 3D geometry whereas the exhaust system, which presented a simpler geometry, was modeled by means of a 1D approach. Predicted 1D and 1D-3D results, concerning pressure pulses in the intake system and volumetric efficiency, were used to guide the design stage in order to improve the engine performances in terms of torque and power output. Calculation carried out on prototyped geometries have been successfully compared to experimental measurements.