Background Based on the hypothesis that pulmonary vein isolation could result in the damage of the epicardial fat pads, this study aimed to investigated the impact of right upper pulmonary vein (RUPV) isolation on vagal innervation to atria.Methods Bilateral cervical sympathovagal trunks were decentralized in 6 dogs. Metoprolol was given to block sympathetic effects. Multipolar catheters were placed into the right atrium (RA) and coronary sinus (CS). RUPV isolation was performed via transseptal procedure. Atrial effective refractory period (ERP), vulnerability window (VW) of atrial fibrillation (AF), and sinus rhythm cycle length (SCL) were measured at RA and distal coronary sinus (CSd) at baseline and vagal stimulation before and after RUPV isolation. Serial sections of underlying tissues before and after ablation were stained with haematoxylin and eosin.Results SCL decreased significantly during vagal stimulation before RUPV isolation (197 ± 21 vs 13 ±32 beats per minute, P＜0.001), but remained unchanged after RUPV isolation (162±29 vs 140±39 beats per minute,P＞0.05). ERP increased significantly before RUPV isolation compared with that during vagal stimulation [(85.00±24.29) ms vs (21.67±9.83) ms at RA, P＜0.001; (90.00± 15.49) ms vs (33.33±25.03) ms at CSd P＜0.005],but ERP at baseline hardly changed after RUPV isolation compared with that during vagal stimulation [(103.33 ±22.50) vs (95.00± 16.43) ms at RA, P = 0.09; (98.33±24.83) vs (75.00±29.50) ms at CSd, P=0.009]. The ERP shortening during vagal stimulation after RUPV isolation decreased significantly [(63.33 ± 22.51) ms vs (8.33 ±9.83) ms at RA, P＜0.005; (56.67±20.66) ms vs (23.33± 13.66) ms at CSd, P＜0.05]. AF was rarely induced at baseline before and after RUPV isolation (VW close to 0), while VW of AF to vagal stimulation significantly decreased after RUPV isolation [(40.00± 10.95) vs 0 ms at RA, P＜0.001; (45.00±32.09) vs (15.00±23.45) ms at CS, P ＜0.05]. The architecture of individual ganglia was significantly altered after ablation.Conclusions The less ERP shortening to vagal stimulation and altered architecture of individual ganglia after right upper pulmonary vein isolation indicate that isolation may result in damage of the epicardial fat pads,thereby attenuating the vagal innervation to atria. The decreased vulnerability window of atrial fibrillation indicates that vagal denervation may contribute to its suppression.