The Bentall procedure, using a composite valve graft, has become one of the standard therapies for aortic root disease. Patients with Marfan syndrome are prone to aortic annular dilatation and dissection and often undergo aortic root replacement, including the Bentall procedure. Therefore, this study aimed to compare the long-term outcomes of the Bentall procedure between Japanese patients with and without Marfan syndrome. Data from 294 patients who underwent the Bentall procedure over 37years were retrospectively analyzed. The study compared the data of patients with Marfan syndrome (n = 94) and those without it (n = 200). Patient characteristics, surgical techniques, and postoperative outcomes were evaluated. Statistical analyses were performed to identify risk factors associated with early mortality, late mortality, reoperation, and aortic root reoperation. The early mortality rate was 4.1%, with no significant difference between patients with and without Marfan syndrome. The long-term survival rates at 10, 20, and 30years were 81.0%, 66.5%, and 49.1%, respectively, with no significant between-group differences. Aortic reoperations were more frequent in patients with Marfan syndrome; however, the number did not differ significantly between the groups. Risk factors for late mortality included diabetes and coronary reimplantation with an inclusion technique. Aortic dissection, Marfan syndrome, and smoking were risk factors for aortic reoperation. Late mortality after the Bentall procedure was comparable between Japanese patients with and without Marfan syndrome although aortic reoperation was significantly frequent in patients with Marfan syndrome. Continuous monitoring and management, including the prevention of aortic dissection and dilation of residual aorta, are crucial for patients with Marfan syndrome undergoing the Bentall procedure.