BACKGROUND: J waves are associated with increased vagal activity in patients with idiopathic ventricular fibrillation in several studies to date. However, the relationship between J waves and autonomic nervous activity in patients without structural heart disease remains under investigation. We investigated whether the presence of a J wave on the surface electrocardiogram (ECG) was related to increased vagal activity in patients without structural heart disease. METHODS: This retrospective study included 684 patients without structural heart disease who had undergone Holter ECG and surface ECG monitoring. Based on the presence of J waves on the surface ECG, patients were divided into two groups: those with J waves (group 1) and those without J waves (group 2). We compared heart rate variability (HRV), reflecting autonomic nervous activity, using 24-h Holter ECG between the groups. RESULTS: J waves were present in 92 (13.4%) patients. Heart rate (HR) in group 1 was significantly lesser than that in group 2 (P = 0.031). The ratio of low-frequency (LF) components to high-frequency (HF) components (LF/HF) in group 1 was significantly lower than that in group 2 (P = 0.001). The square root of the mean squared differences of successive NN intervals in group 1 was also significantly higher than that in group 2 (P = 0.047). In a multivariate regression analysis, male sex, HR, and LF/HF ratio remained independent determinants for the presence of J waves (P = 0.039, P = 0.036, and P < 0.001, respectively). CONCLUSION: In patients without structural heart disease, the presence of a J wave was associated with a slow HR, male sex, and increased vagal activity, independently.