Background: Cardiac arrhythmias including atrial fibrillation are a leading cause of death and disability from stroke. Atrial F wave is very weak and uneven to detect, so it is difficult to trace its abnormal conduction route using conventional EKG method. Electrophysiology study is still very invasive, hard and time-consuming procedure to both patient and physician. Magnetocardiography action potential mapping is a totally-noninvasive, non-contact method to detect atrial F wave for source localization. We report the clinical application cases of MCG map-guided minimal AF surgery. Methods: To detect weak atrial excitation, we utilized a high sensitive low-Tc 64-channel MCG system with application software KRISSMCG64 to make a MCG map on the three-dimensional atrial surface. From the Activity Maps of the Action Potential at the sequential time instants, we can infer the propagation trace of the atrial excitation. Using this information, we conducted minimal AF surgery in six patients with Rt PV isolation only, 3/4 PV isolation + minimal RA procedure, minimal RA procedure only, 1/2 PV isolation + minimal RA procedure, 1/2 PV isolation + minimal LA, RA procedure and LAA + RA linear procedure respectively. Results: From June 2005 to July 2007, we localized the abnormal stimulation source of an atrial arrhythmia non-invasively and visualized the current source distribution corresponding to the atrial excitation successfully on the three-dimensional atrial surface in 8 from 17 patients. Among them, we underwent MCG-map guided minimal AF surgery in six patients and converted their AF to regular rhythm successfully in 4 patients with follow-up period of 408 days, 205 days, 21 days and 99 days respectively. Conclusions: MCG is a totally noninvasive and even non-contact method for analyzing atrial arrhythmia and would be a great help for planning the AF treatment and for the follow-up examination. MCG map-guided minimal AF surgery might be a new method to treat AF.