Intense competition and global regulations in the automotive industry has placed unprecedented demands on the performance, efficiency, and emissions of today's IC engines. The success or failure of a new engine design to meet these often-conflicting requirements is primarily dictated by its capability to provide minimal restriction for the inducted and exhausted flow and by its capability to generate strong large-scale in-cylinder motion. The first criterion is directly linked to power performance of the engine, while the latter has been shown to control the burn rate in IC engines. Enhanced burn rates are favorable to engine efficiency and partial load performance. CFD based Numerical Simulations have recently made it possible to study the development of such engine flows in great details. However, they offer little guidance for modifying the ports and chamber geometry controlling the flow to meet the desired performance. This paper presents a methodology which combines three-dimensional, steady state CFD techniques with robust numerical optimization tools to design, rather than just evaluate the performance, of IC engine ports and chambers. Various optimization problems are solved in this study to define a tradeoff relationship between the engine flow resistance and its capability to generate large-scale in-cylinder motion. Such a trade-off curve can provide engine designers with invaluable information to meet specific engine performance objectives. The methodology is illustrated through the design of an intake port of a typical two-valve IC engine.