Background: The ectopic foci originating from superior vena cava (SVC) may act as triggers in the occurrence and perpetuation of atrial fibrillation (AF). Unfortunately, the SVC isolation may result in potential dysfunction of sinus node. Furthermore, little is known about the occurrence of sinus node injury complicated by the SVC isolation. Methods: Patients with AF or atypical atrial flutter experienced SVC isolation. The junctional rhythm or sinus arrest could be observed, if sinus node was injured. Atropin and dopamine administration ruled out the vagal irritation of sinus node, when junctional rhythm or sinus arrest occurred. Results: One hundred and thirty-two patients who had no electrocardiogram signs of sinus node dysfunction before ablation experienced the SVC isolation. Six patients (three men, three women, mean age 62.5 ± 8.6 years) had sinus node injury (4.5%, 6/132): four patients had junctional rhythm and one male patient had junctional rhythm and sinus arrest simultaneously; another male patient required AAI mode permanent pacemaker implantation due to the persistent junctional rhythm after SVC isolation. The ablation sites of all six patients closed to the junction of right atrium and SVC during the ablation of anterolateral free wall of the SVC. Conclusion: Sinus node may be damaged due to the ablation sites closer to sinus node. The definition of the junction of right atrium and SVC is very important, the ablation sites of anterolateral free wall of the SVC should not be too close to the SVC orifice. © 2010 Wiley Periodicals, Inc.