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Background: The occurrence of aorto-right atrial fistula in a patient with Stanford type A aortic dissection is exceedingly rare, and the treatment has not been established. Case presentation: A 60-year-old male presented to the emergency department with acute lumbar pain and, based on contrast-enhanced computed tomography, was diagnosed with Stanford type A aortic dissection. Emergency surgery was performed. Transesophageal echocardiography during the surgery did not reveal an aorto-right atrial fistula. After establishing cardiopulmonary bypass, circulatory arrest was induced, and the primary entry in the proximal ascending aorta for the aortic dissection was identified. The aorta was dissected between the right brachiocephalic artery and the left common carotid artery, and an artificial conduit was anastomosed. After re-establishing circulation, venous blood flow from the dissected area at the base of the aortic root was observed, indicating communication between the aorta and the right atrium. Circulatory arrest was induced again, and the ruptured outer aortic adventitia was repaired by continuous suturing using 5–0 prolene. The atrial fistula was repaired from within the right atrium using 5–0 prolene with felt reinforcement. Thus, successful closure was achieved. Proximal anastomosis and right brachiocephalic artery reconstruction were subsequently performed. Postoperative transesophageal echocardiography revealed no shunt flow and no bleeding from the aortic root. The patient recovered smoothly and was discharged without significant complications. Conclusions: Aorto-right atrial fistula associated with Stanford type A aortic dissection is rare, and in this case, the shunt blood flow was low, making preoperative diagnosis difficult. However, after intraoperative diagnosis, direct suture was used to complete the treatment, which was a simple and effective method. [ABSTRACT FROM AUTHOR]