Introduction: Respiratory sinus arrhythmia (RSA) describes heart rate (HR) changes in synchrony with respiration. It is relevant for exercise capacity and mechanistically linked with the cardiac autonomic nervous system. After pulmonary vein isolation (PVI), the current therapy of choice for patients with paroxysmal atrial fibrillation (AF), the cardiac vagal tone is often diminished. We hypothesized that RSA is modulated by PVI in patients with paroxysmal AF. Material and methods: Respiratory sinus arrhythmia, measured by using a deep breathing test and heart rate variability parameters, was studied in 10 patients (64 ±3 years) with paroxysmal AF presenting in stable sinus rhythm for their first catheter-based PVI. Additionally, heart rate dynamics before and after PVI were studied during sympathetic/parasympathetic coactivation by using a cold-face test. All tests were performed within 24 h before and 48 h after PVI. Results: After PVI RSA (E/I difference: 7.9 ±1.0 vs. 3.5 ±0.6 bpm, p = 0.006; E/I ratio: 1.14 ±0.02 vs. 1.05 ±0.01, p = 0.003), heart rate variability (SDNN: 31 ±3 vs. 14 ±3 ms, p = 0.006; RMSSD: 17 ±2 vs. 8 ±2 ms, p = 0.002) and the HR response to sympathetic/parasympathetic coactivation (10.2 ±0.7% vs. 5.7 ±1.1%, p = 0.014) were diminished. The PVI-related changes in RSA correlated with the heart rate change during sympathetic/parasympathetic coactivation before vs. after PVI (E/I difference: r = 0.849, p = 0.002; E/I ratio: r = 0.786, p = 0.007). One patient with vagal driven arrhythmia experienced AF recurrence during follow-up (mean: 6.5 ±0.6 months). Conclusions: Respiratory sinus arrhythmia is reduced after PVI in patients with paroxysmal AF. Our findings suggest that this is related to a decrease in cardiac vagal tone. Whether and how this affects the clinical outcome including exercise capacity need to be determined.