Background It has been known that radiofrequency catheter ablation (RFCA) of atrial fibrillation (AF) changes cardiac autonomic nerve function measured by heart rate variability (HRV). We hypothesized that degree of left atrial (LA) structural remodeling and P wave morphology in electrocardiography (ECG) are related with post-RFCA 3rd month HRV or frequency of 24hour-atrial premature beats (fAPC). Methods We obtained 24-hour Holter ECG in 103 patients (87 males, 54.32210.898 years old) who underwent RFCA for AF (72 paroxysmal AF, 31 persistent AF). The results of HRV were compared with pre-ablation echocardiography, pre- and post-ablation ECG, and fAPC. Results 1. Patients who had low frequency (LF)/ high frequency (HF) domain ratio  1.5 had greater LA size (42.05짹4.62mm vs 39.29짹10.61mm, p=0.007), left ventricular end-diastolic dimension LVEDD (51.14짹4.03mm vs. 47.76짹12.65mm, p=0.016), and longer P wave duration (103.97짹16.25ms vs. 97.2짹26.84ms, p=0.022) than those with LF/HF ratio<1.5. 2. HF domain which is related with parasympathetic tone was negatively correlated with post-RFCA P wave duration (R=-0.21, CI -0.197~-0.005, p=0.039), P wave amplitude (R=-0.22, CI -104.186~-4.478, p=0.033), and positively correlated with PR interval (R=0.29, CI 0.023~0.118, p=0.004). 3. In patients who had recurred AF after 3rd month blanking period (8/103; 7.8%) during 11.01.2 months follow-up, HF domain (16.116.4 vs. 7.35.3, p<0.001), LF domain(25.433.0 vs. 10.311.3, p<0.001), fAPC (3082.34417.9/day vs. 518.11388.6/day, p<0.001) and maximal heart rate (132.929.4bpm vs. 117.820.9bpm, p=0.032) were higher and pre-RFCA P wave duration were longer (116.07.9ms vs. 102.015.2ms, p=0.009) than those without recurrence. Conclusion Post-RFCA 3rd month HRV is associated with inter-atrial conduction time, atrial muscle mass and LA size in patients with AF. Post-RFCA high HF domain, high LF domain, high maximal heart rate, high fAPC and long pre-ablation inter-atrial conduction time were related to clinical recurrence of AF 3 months later after RFCA. It suggests post-AF ablation HRV is associated with pre-existing electrical and structural remodeling of atria.