This work reports a CFD study on a 2-stroke (2-S) opposed piston high speed direct injection (HSDI) Diesel engine. The engine main features (bore, stroke, port timings, et cetera) are defined in a previous stage of the project, while the current analysis is focused on the assembly made up of scavenge ports, manifold and cylinder. The first step of the study consists in the construction of a parametric mesh on a simplified geometry. Two geometric parameters and three different operating conditions are considered. A CFD-3D simulation by using a customized version of the KIVA-4 code is performed on a set of 243 different cases, sweeping all the most interesting combinations of geometric parameters and operating conditions. The post-processing of this huge amount of data allow us to define the most effective geometric configuration, named baseline.In the second step of the study, the baseline is further optimized, keeping into account some fundamental design constraints, such as the overall dimensions of the manifold. The evolved geometry is then simulated by using KIVA, adopting a refined grid and realistic boundary conditions. The paper presents the calculated scavenging patterns, offering a detailed insight of the process.Finally, the influence of the offset between the crankshafts is analyzed, by using a calibrated CFD-1D engine model.