The aim of the study was to assess the safety and efficacy of thoracoscopic microwave ablation in treating atrial fibrillation (AF). AF predisposes to embolic complications and may cause heart failure. The treatment of AF is still challenging in spite of the promising results of endocardial radiofrequency approach. The present study is a follow-up study of 22 patients (mean age 45 years, range 21-59) with disabling paroxysmal (n=10) or persistent (n=12) AF who underwent a thoracoscopic microwave isolation of pulmonary veins. The patients had a lone AF. All the patients had suffered from severely disabling AF for >1 year (range 1-16 years) without any response to antiarrhythmic medication. The patients have been followed-up on an average of 11 months (range 3-22 months). During the follow-up, 13 (60%) patients have become asymptomatic without any documentation of AF since at least two months, six (27%) patients with anti-arrhythmic medication have clinically improved. Because of major intrathoracic bleeding and because of liver damage the thoracoscopy wound had to be expanded to open thoracotomy in two patients. Thoracoscopic AF microwave ablation seems to be a promising alternative to endocardial ablation in the treatment of highly symptomatic paroxysmal and persistent AF.