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Background: Hypertrophic cardiomyopathy (HCM) is often accompanied by atrial fibrillation (AF) due to diastolic dysfunction, elevated left atrial pressure, and enlargement. Although catheter ablation for drug-refractory AF is an effective treatment, the efficacy in HCM remains to be established., Methods: Thirty-three consecutive patients (25 male, age 51 +/- 11 years) with HCM underwent pulmonary vein (PV) isolation (n = 8) or wide area circumferential ablation with additional linear ablation (n = 25) for drug-refractory AF. Twelve-lead and 24-hour ambulating ECGs, echocardiograms, event monitor strips, and SF 36 quality of life (QOL) surveys were obtained before ablation and for routine follow-up., Results: Twenty-one (64%) patients had paroxysmal AF and 12 (36%) had persistent/permanent AF for 6.2 +/- 5.2 years. The average ejection fraction was 0.63 +/- 0.12. The average left atrial volume index was 70 +/- 24 mL/m(2). Over a follow-up of 1.5 +/- 1.2 years, 1-year survival with AF elimination was 62%(Confidence Interval [CI]: 66-84) and with AF control was 75%(CI: 66-84). AF control was less likely in patients with a persistent/chronic AF, larger left atrial volumes, and more advanced diastolic disease. Additional linear ablation may improve outcomes in patient with severe left atrial enlargement and more advanced diastolic dysfunction. Two patients had a periprocedureal TIA, one PV stenosis, and one died after mitral valve replacement from prosthetic valve thrombosis. QOL scores improved from baseline at 3 and 12 months., Conclusion: Outcomes after AF ablation in patients with HCM are favorable. Diastolic dysfunction, left atrial enlargement, and AF subtype influence outcomes. Future studies of rhythm management approaches in HCM patients are required to clarify the optimal clinical approach.