The effectiveness of scavenging, the displacement of residual combustion gases with fresh air, is examined in an advanced, high power-density diesel engine, consisting of a two-stroke, opposed-piston reciprocator with an ultra-high boost. KIVA-3, a three-dimensional code for modeling reactive flows with fuel injection, is used to study the effect of a variety design choices on scavenging. The parametric study includes the inclined angle of the intake ports, the exhaust port timing and size and the piston stroke-to-bore ratio. A baseline geometry of the opposed-piston engine is examined in detail, which models an existing mono-cylinder test rig. The baseline-design exhibits large asymmetries, nonsteady flow and large recirculation regions that degrade the scavenging. Significant improvement in the scavenging of the baseline design is observed with a uniform inclined angle of the inlet ports of about 20° and with a larger stroke-to-bore ratio (2.0 compared with 1.08).