Previous studies have reported that metabolic syndrome (MS) is associated with the development of atrial fibrillation (AF). However, its impact on the atrial substrate properties and catheter ablation in patients with AF is still unclear. This study consisted of 282 patients with AF (216 with paroxysmal AF and 66 with nonparoxysmal AF) who underwent catheter ablation using a 3-dimensional mapping system (NavX). Detailed AF mapping (frequency analysis and complex fractionated electrographic mapping) was performed in 59 patients. The patients were classified on the basis of MS, which was defined according to the guidelines of the National Cholesterol Education Program Adult Treatment Panel III. Patients with MS had larger left atrial sizes, shorter fractionated intervals, and higher dominant frequencies compared with those without it. Higher incidences of complex fractionated atrial electrographic sites located in the left atrial appendage base, coronary sinus, and crista terminalis regions were found in patients with MS. Patients with MS had a higher incidence of recurrent AF compared with those without MS (55% vs 24%, p <0.001). A higher incidence of recurrent AF from non-pulmonary vein origins was observed in patients with MS compared with those without it (45% vs 20%, p = 0.037). In conclusion, MS is associated with larger left atrial size and an arrhythmogenic substrate, which may increase the risk for recurrence after the ablation of AF. Close follow-up with good control of any metabolic disturbances may be needed in patients with MS to improve their outcomes after AF ablation.