BACKGROUND: Different surgical techniques for creating a Fontan circulation can be used. The option of including an atrium in the circuit, or the technique used for connecting the caval veins to the pulmonary artery in a total cavopulmonary connection, frequently is empirical and is based on personal experience and preference. The hemodynamic and energetic differences between the different circuits are small, and short-term results are comparable. However, small, energetic differences may have significant implications for the long-term follow-up. The finite element method allows a computer-based modeling of the flow dynamics and pressure losses. It permits comparison of different Fontan connections in a single patient with identical geometry and functional conditions. METHODS AND RESULTS: We compared the atriopulmonary connection with different types of cavopulmonary connections, which differed in the degree of symmetry of implantation of both caval veins into the right pulmonary artery. Based on anatomic models and physiological flow dynamics, three-dimensional geometries and finite element meshes were created with PATRAN; flows were calculated with POLYFLOW (B), and results were visualized with DATA VISUALIZER. CONCLUSIONS: The atriopulmonary connection produces higher energy losses than the cavopulmonary connection (+/- 1 mm Hg at rest). The cavopulmonary connection is more efficient when the connection of the caval veins to the pulmonary artery is asymmetrical.