Background This study aimed to evaluate the relationship between dominant frequencies (DFs)/rotors and low-voltage areas (LVAs) using the Advisor HD grid (HDG) after pulmonary vein isolation (PVI) in non-paroxysmal atrial fibrillation (AF). Methods A total of 73 non-paroxysmal AF patients were prospectively investigated. After pulmonary vein isolation (PVI), an online real-time phase mapping system was used to detect the location of rotors with critical non-passively activated ratios (%NPs) of≧50% in each LA segment, and high-DFs of ≧7Hz were simultaneously mapped. After recovering sinus rhythm, LVAs (<0.5mV) were mapped using the HDG. Results Sixty-eight of 73 (93.2%) AF patients had minimum to mild LVAs (<10%) regardless of an enlarged LAD and LA volume (45±6.1mm and 142±30ml). There were no significant differences in the max and mean DF values and %NPs between the patients with and without recurrent AF/AT (atrial tachycardia). However, LVAs were significantly greater in the patients with AF/AT than in those without (6.4±8.0% vs. 2.5±2.6% P=0.003). Furthermore, the number of high-DF sites overlapping with LVAs was significantly greater in the patients with AF/AT than in those without (0.5±0.8 vs. 0.2±0.7, P=0.019). The AF/AT freedom off anti-arrhythmic drugs after the PVI was significantly lower in the patients with high-DFs sites overlapping with LVAs than in those without during 11.6±0.8 months of follow-up (35.7% vs. 69.5%, p=0.021). Conclusions High-DF sites overlapping with LVAs detected accurately by the HDG, regardless of whether a minimum to mild extent, might be more selective targets after a PVI in non-paroxysmal AF patients.