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Objectives: We examined the role of atrial gap junctions, NF-κB and fibrosis in the occurrence of postoperative atrial fibrillation (AF) in patients undergoing coronary artery bypass graft (CABG) surgery. Methods: Forty-five patients with sinus rhythm were randomly assigned to the beating heart (n = 22) or cardioplegic cardiac arrest (n = 23) technique for surgery. Of them, 14 patients experienced post-CABG AF. Atrial samples taken before and after CABG surgery were analyzed. Results: During surgery, Cx43 and Cx40 proteins were significantly reduced (both p < 0.05) in the arrested heart group, but only mildly decreased in the beating heart group. However, the change of either connexin was not associated with AF. In contrast, patients with AF had a higher baseline expression of NF-κB and more fibrosis compared to those without AF (both p < 0.05). Conclusions: CABG surgery with the beating heart technique attenuated the reduction of atrial Cx43 and Cx40 compared to the cardioplegic cardiac arrest technique. Atrial inflammation and fibrosis status before surgery, but not the changes of connexins during surgery, were associated with the occurrence of post-CABG AF.