Diabetes mellitus has been reported to be an independent risk factor of atrial fibrillation (AF). The present study investigated the atrial substrate properties and clinical outcome of catheter ablation in patients with paroxysmal AF and abnormal glucose metabolism. A total of 228 patients with paroxysmal AF who had undergone catheter ablation for the first time were enrolled. An abnormal glucose metabolism (n = 65) was defined as diabetes mellitus or an impaired fasting glucose. We analyzed the clinical and electrophysiologic characteristics in, and the clinical outcome of, patients with AF with and without an abnormal glucose metabolism. The right atrial (107.2 ± 15.4 vs 96.0 ± 16.5 ms, p <0.001) and left atrial (108.4 ± 22.3 vs 94.0 ± 17.5 ms, p <0.001) total activation times were significantly longer in the patients with AF and an abnormal glucose metabolism than in those without an abnormal metabolism. Furthermore, the right atrial (1.46 ± 0.61 vs 2.00 ± 0.70 mV, p <0.001) and left atrial (1.48 ± 0.74 vs 2.05 ± 0.78 mV, p <0.001) bipolar voltages were significantly lower in those with AF and an abnormal glucose metabolism than in those without. The AF recurrence rate was also greater in the patients with an abnormal glucose metabolism (18.5% vs 8.0%, p = 0.022) than in those without. The follow-up duration was 18.8 ± 6.4 months. In conclusion, an abnormal glucose metabolism affects the biatrial substrate properties with an intra-atrial conduction delay, decreased voltage, and greater recurrence rate after catheter ablation.