Background: Modulation of the intrinsic cardiac autonomic nervous system (ICANS) can occur after radiofrequency (RF) pulmonary vein isolation (PVI) for atrial fibrillation (AF). However, the effects of cryoballoon (CB) ablation and hot-balloon (HB) based PVI on the ICANS have not been evaluated. We compared the acute periprocedural effects on the ICAVS, as well as changes in heart rate variability (HRV) between RF-, CB-and HB-based PVI. Methods: The vagal response to high-frequency stimulation (25 Hz, 20 mA, 10 ms) applied to 5 major left atrial (LA)-ganglionated plexi (GP) before and after assessment of PVI in 31 patients with CB-PVI, 16 patients with HB (SATAKE Hot-BalloonTM, Toray, Tokyo, Japan), and 18 patients with RF-PVI. Among 47 patients (21: CB-PVI, 16: HB-PVI, and 10: RF-PVI) with sinus rhythm on admission, HRV was assessed for 5 minutes 1 day before and 2 days after PVI using high-resolution ECG (HRES-1000, FUKUDA DENSHI, Tokyo, Japan). Results: In the RF, CB and HB groups, 72%, 73% and 78% of the LA GPs were ablated. (P = 0.5018: N.S.) The change in heart rate (ΔHR) after PVI was increased significantly in the CB (+13.2 ± 7.1/min; P < 0.001), and HB groups (15.0 ± 8.0/min; P < 0.0001), but the HR did not change significantly in the RF group (+6.5 ± 11.3/min; P = N.S.). Conclusion: RF-, CB and HB-based PVIs affected the LA GPs response to a similar extent, but subsequent changes in heart rate exhibited different patterns between catheter-and balloon-based ablation.