Hypertrophic cardiomyopathy (HCM) represents a common inherited cardiac disorder with well-known complications including stroke and sudden cardiac death. There is a recognised association between HCM and the development of AF. This review describes the epidemiology of AF within the HCM population and analyses the risk factors for the development of AF. It further discusses the outcomes associated with AF in this population, including the evidence in support of higher stroke risk in patients with HCM with AF compared with the general AF population. Finally, the evidence and recommendations for anticoagulation in this patient group are addressed.