To understand the local fluid dynamics for different designs of Fontan operation, five models were made of Pyrex glass to facilitate in vitro study. Models I, II and III had the same position as the center of the anastomosis of the IVC (inferior vena cava) with that of the SVC (superior vena cava), but Models IV and V had 10 mm offset between them. As well, the anastomotic junction angles were different (Models I and IV: 90 °, Models II and V: 70 °, Model III: 45 °). These models were then connected to a flow loop for flow visualization study. In Model I, no dominant vortex was seen in the central region of the junction, but a large unstable vortex was created in Models II and III. In Models IV and V, a significant stagnation region was created in the middle of the offset region. It also showed that the flow distribution from the IVC and SVC to the LPA (left pulmonary artery) and RPA (right pulmonary artery) depends more on the offset of the junction than on the anastomotic junction angle. Generally, as the total flow rates increased, the pressures in the models increased.