Objective: The introduction of ablation technology has simplified surgical intervention for atrial fibrillation. However, most ablation devices cannot create focal transmural lesions on the beating heart and have difficulty ablating specific regions of the atria, such as the atrioventricular isthmus, coronary sinus, and ganglionated plexus. The purpose of this study was to examine the efficacy of a pen-type bipolar radiofrequency ablation device on both arrested and beating hearts. Methods: Endocardial and epicardial atrial tissues in the free wall, left atrial roof, atrioventricular annuli, and coronary sinus were ablated for varying time intervals (2.5-15 seconds) in porcine cardioplegically arrested (n = 6) and beating (n = 9) hearts. The hearts were stained with 1% 2,3,5-triphenyl-tetrazolium chloride solution and sectioned to determine lesion depth and width. In 5 animals epicardial fat pads containing ganglionated plexus were stimulated and ablated. Results: Lesion depth increased with ablation time similarly in both arrested and beating hearts. Transmurality was fully achieved in the thin atrial tissue (<4 mm) at 10 seconds in the beating and arrested hearts. The device had a maximal penetration depth of 6.1 mm. Epicardial ablation of the coronary sinus showed complete penetration through the left posterior atrium only in the arrested heart. Seven of 17 fat pads demonstrated a vagal response. All vagal responses were eliminated after ablation. Conclusion: The bipolar pen effectively ablated atrial tissue in both arrested and beating hearts. This device might allow the surgeon to ablate tissue in regions not accessible to other devices during atrial fibrillation surgery.