Objective To compare the outcome of ablation of atrial fibrillation (AF) between ganglionated plexi (GP) positive and negative and investigate the possible underlying mechanism. Methods Between September 2007 and May 2009, 209 patients (63 males and 146 females) with age of (53±10) (ranging from 24 to 77) years undergoing radiofrequency ablation for AF in our hospital were enrolled in this study. Intraoperative high-frequency stimulation showed that positive vagal reflex was seen in 103 patients and negative in 106 patients. Their average history of AF was (36±43) months. Preoperatively, 144 patients (68.9%) were in New York Heart Association (NYHA) functional class Ⅲ or Ⅳ. They were followed up for (18.9±9.0) (ranging from 6 to 34) months. Results There was no in-hospital death, and no significant difference in mortality or incidence of complications between the 2 groups during the postoperative or follow-up period. The Kaplan-Meier survival curve indicated that 60.8% of patients had freedom from AF, with a higher percentage in the patients with positive vagal reflex than those with negatives (68.2% vs 53.3%, P＝0.0004). Cox analyses identified positive vagal reflex as another predictor of late recurrence of AF besides left atrium size (Wald＝9.71, P＝0.002, 95% CI: 0.081 to 0.563]. ). Vagal reflex and left atrium size were 2 predictors affecting each other (Wald＝4.45, P＝0.035, 95% CI: 0.965 to 0.999). There were more patients with left atrial dimension ＞70mm in the patients with negative vagal reflex than in those with positives (48.1% vs 30.1%, P＝0.008). Conclusion Vagal reflex plays an important role in the maintenance of AF, and denervation will improve converting AF to a normal rhythm. Vagal reflex is another predictor of late recurrence of AF besides left atrium size, and is significantly correlated with the latter. The left atrium size is smaller in patients with positive vagal reflex than in those with negatives.