Recent studies suggest that pulmonary vein isolation can be an effective method of treatment for atrial fibrillation. This procedure can be performed with minimally invasive, totally endoscopic cardiac surgical techniques. We report our first successful endoscopic isolation of the pulmonary veins in a patient with paroxysmal atrial fibrillation. The procedure consisted of making a box lesion around the pulmonary veins, using a flexible microwave energy delivery probe which was placed endoscopically (video assisted thoracoscopy) through three ports, bilaterally. During a six-month follow up there was no recurrence of atrial fibrillation and the patient's quality of life improved significantly.