Atrial fibrillation (AF) is the most common sustained arrhythmia in patients with hypertrophic cardiomyopathy (HCM), and represents an important complication in the clinical course of the disease, with adverse consequences on functional status and outcome. Studies on community-based HCM patient populations have shown that AF is associated with long-term clinical deterioration, cardioembolic stroke and increased cardiovascular mortality due to heart failure and stroke. Moreover, acute onset of AF may cause severe hemodynamic impairment and represent a trigger of potentially lethal ventricular arrhythmias. However, the consequences of AF on the long-term prognosis of HCM patients are not uniformly unfavorable, and may be compatible with an uneventful course, when properly managed. Management of AF in HCM is challenging, particularly when onset occurs at a young age. Both paroxysmal and permanent AF represent clear indications for oral anticoagulation. In most patients, maintenance of sinus rhythm is highly desirable but made difficult by the limited long-term efficacy and potentially hazardous side effects of available pharmacological options. In selected patients with HCM and severely symptomatic AF, radiofrequency catheter ablation may represent an effective therapeutic alternative, improving functional status, and reducing or postponing the need for antiarrhythmic drugs. In patients with persistent AF, in whom maintenance of sinus rhythm is not feasible, adequate ventricular rate control should be pursued aggressively by atrio-ventricular node blocking agents.