OBJECTIVE: To compare the incidence of atrial fibrillation (AF) and alteration of heart rate variability (HRV) after pulmonary lobectomy through video assisted thoracic surgery or thoracotomy, and to explore the role of autonomic nerves in the pathogenesis of atrial fibrillation after pulmonary lobectomy. METHODS: In a single institution, 224 patients (age > 60) with normal sinus rhythm were enrolled in the study. Experienced surgeons and anesthetists carried out operation and anesthesia according to the same procedure. The hearts were monitored using Holter for more than 96 h. Any new-onset AF was recorded and HRV was analyzed at different time intervals. RESULTS: One hundred twelve patients undergoing video-assisted thoracic surgery (VATS) and 112 patients undergoing thoracotomy (THOR) were matched for age and gender. Atrial fibrillation occurred in 39 patients, with a similar incidence between the two groups (VATS: 19/112, 16.9% and THOR: 20/112, 17.9%, P = 0.82). The post-operational heart variability at different time intervals was comparable between the two groups. CONCLUSION: Pulmonary lobectomy through video assisted thoracic surgery does not reduce the postoperative atrial fibrillation. Autonomic nerve mechanism may be involved in the pathogenesis of postoperative atrial fibrillation.