Prevalent atrial fibrillation (AF) in patients with hypertrophic cardiomyopathy (HCM) represents an important issue with regard to stroke events caused by embolization and is associated with high mortality. Increased epicardial adipose tissue (EAT), which shows high metabolic activity, can locally influence the activity of the autonomic ganglia, enhancing autonomic dysregulation and increasing the likelihood of AF. We tested the hypothesis that EAT is associated with prevalent AF in HCM patients. Sixty-two patients with idiopathic HCM diagnosed on the basis of ultrasound cardiography findings and histopathological evaluation of myocardium obtained by right ventricular biopsy underwent cardiac magnetic resonance imaging to estimate the extent of EAT. EAT area was significantly higher in the group with AF episodes than in the group without. An increased incidence of AF was found to be significantly related to an increase in EAT, and this association persisted after adjustment for body mass index, sex, and age. Time domain measures of heart rate variability measured by Holter electrocardiography, standard deviation of normal to normal, and standard deviation of the average of normal to normal were negatively related to EAT area. EAT was positively correlated with intraventricular septal thickness and cystatin C level and negatively correlated with the 24-hour creatinine clearance rate. Increased EAT area in HCM patients is significantly related to the presence of AF, which is associated with changes in baseline autonomic nervous tone, left ventricular mass, and chronic kidney disease.