AIMS: The efficacy of catheter-based pulmonary vein isolation (PVI) for paroxysmal atrial fibrillation (AF) and prolonged sinus pauses [bradycardia-tachycardia syndrome (BTS)] has been already described. However, the effects of PVI on autonomic modulation in BTS patients remain to be determined. We, therefore, examined the alteration in the autonomic modulation through the PVI procedure by using a heart rate variability (HRV) analysis of 24 h ambulatory monitoring. METHODS AND RESULTS: This study consisted of 26 symptomatic paroxysmal AF patients either with prolonged sinus pauses on termination of AF (>3.0 s, BTS group, n = 11) or without any evidence of sinus node dysfunction (control group, matched for sex and age, n = 15) who underwent PVI. All 11 BTS patients became free from both AF and prolonged sinus pauses without pacemaker implantation (23 +/- 14 months of observation). The mean heart rate significantly increased in the control group (P < 0.05), but not in the BTS group after the PVI procedure, although the HRV parameters of root-mean-square successive differences in the adjacent NN intervals, standard deviation of the NN intervals, and high frequency did significantly decrease in both groups (P < 0.05). CONCLUSION: Although the parasympathetic modulation was significantly attenuated after the PVI procedure, the mean heart rate did not increase in the BTS patients, probably due to the pre-existing sinus node dysfunction.