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Apical hypertrophic cardiomyopathy (ApHCM) is considered a ‘benign’ form of hypertrophic cardiomyopathy, with limited data on the long-term outcome. However, the clinical impact of atrial fibrillation (AF) in ApHCM is largely unknown. The hypothesis was that AF is common and has a prognostic implication in ApHCM.The occurrence of AF and outcome was assessed in 306 consecutive patients with ApHCM (68% male, 62±11 years).AF occurred in 77 patients with ApHCM (prevalence, 25.2%; annual incidence, 4.6%/year) and was independently predicted by old age and large left atrium (>45 mm). Among 70 AF patients indicated with anticoagulation, 53 patients (76%) received warfarin. During a follow-up of 5.5±2.0 years, the patients with AF had a higher incidence of all-cause death, cardiovascular death and strokes (11.7% vs 1.3%, 6.5% vs 0.9% and 19.5% vs 2.6%, respectively, all p<0.05) than those without AF. When adjusted by the age and gender, those with AF still had an increased risk for all-cause death (HR 6.58; 95% CI 1.65–26.16, p=0.007) and strokes (HR 5.13; 95% CI 1.85 to 14.18, p=0.002). AF was detected before the time of stroke in 8 (53%) out of 15 patients with both AF and stroke. In addition, six out of eight patients were on anticoagulation at the time of stroke. The cause of death was a stroke in three (33%) out of nine patients with AF.In patients with ApHCM, AF was common and was associated with a substantial risk for strokes and mortality suggesting that AF should be carefully managed in ApHCM.