Background: The association of atrial fibrillation (AF) with sudden death and the difference in prognostic significance between paroxysmal and non-paroxysmal AF remains unclear in patients with hypertrophic cardiomyopathy (HCM). Our aim was to investigate the clinical significance of AF, and to assess the prognostic difference between paroxysmal and non-paroxysmal AF in HCM patients. Methods: The study included 430 HCM patients. Documentation of AF was based on electrocardiograms obtained either after the acute onset of symptoms or fortuitously during routine examination of asymptomatic patients. Results: AF was detected in 120 patients (27.9%). In the patients with AF, syncope and non-sustained ventricular tachycardia were more frequent and the left atrial dimension was larger. Multivariate analysis showed that AF was an independent determinant of the outcome, including the risk of HCM-related death (adjusted hazard ratio 3.57, p < 0.001) and sudden death (adjusted hazard ratio 2.61, p = 0.038). When patients with AF were divided into subgroups with paroxysmal AF (n = 75) or non-paroxysmal AF (n = 45), only paroxysmal AF was identified as an independent determinant of the outcome, including the risk of HCM-related death (adjusted hazard ratio 5.24, p <0.001) and sudden death (adjusted hazard ratio 4.67, p = 0.002). Conclusions: AF is a common supraventricular arrhythmia in HCM and has an adverse influence on the prognosis. In addition, each type of AF had a different clinical impact, with paroxysmal AF being a significant independent determinant of an adverse outcome, including sudden death. (c) 2013 Japanese College of Cardiology. Published by Elsevier Ltd. All rights reserved.