The relationship between autonomic nerve system and the onset of paroxysmal atrial fibrillation (PAF) is still controversial. Furthermore, no prior studies have compared heart rate variability (HRV) between PAF patients with (organic) or without (idiopathic) underlying cardiac diseases. The purpose of this study was to assess the alteration of autonomic tone by analyzing HRV immediately before the onset of atrial fibrillation. This study included 57 patients (M/F: 34/23, 66+/-22 years) with frequent attacks of PAF. All cases underwent 24-h ambulatory Holter monitoring; each patient had one or more episodes of sustained PAF (>30 s). A period of sinus rhythm 40 min was allowed for accurate assessment of HRV over these periods. Spectral HRV was expressed as low (0.04-0.15 Hz) and high (0.15-0.40 Hz) frequency components (LF, HF), and L/H ratio at 2-min intervals over a 40-min period before the onset of PAF. According to HRV, three subtypes were classified; onset of PAF accompanied with increased HF component and decreased L/H ratio was designated as vagal type; decreased HF component and increased L/H ratio was designated as sympathetic type, and the other episodes which did not belong to vagal or sympathetic type were designated as non-related type. In group I (idiopathic PAF, n=30): 63 episodes of PAF were found and vagal type was predominant (41/63, 63.5%); HF increased significantly before the onset of AF. In group II (organic PAF, n=27): 58 episodes of PAF were found and sympathetic type was predominant (39/58, 67.2%); L/H ratio increased before AF onset. None of the three subtypes showed significant circadian distributions in group I and II patients. Changes of HRV before the onset of PAF were not universal; most of the patients with idiopathic PAF were vagal dependent and most of the patients with organic PAF were sympathetic dependent.