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Hypertrophic cardiomyopathy (HCM) is an inherited myocardial disease associated with atrial fibrillation (AF) and thromboembolism (TE), which are related to adverse clinical outcomes and reduced survival. Current ESC and ACCF/AHA guidelines recommend anticoagulation in all patients with HCM and atrial fibrillation but the absolute risk of thromboembolism in patients with and without documented AF is unclear. The primary aim of this study was to derive and validate a model for estimating the risk of TE in HCM. Analyses were performed to determine predictors of AF and TE. Exploratory analyses assessed the performance of the CHA2DS2-VASc score and outcome with vitamin K antagonists (VKA). A further aim was to investigate the effect of AF on mortality and the efficacy of antiarrhythmic therapy in the development of AF.