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Hypertrophic cardiomyopathy (HCM) is the most common congenital disease increasing the risk of sudden cardiac death. For many years, HCM patients were excluded from exercise training. However, there are data showing that patients with HCM undergoing supervised exercise training could improve physical performance without serious adverse events. A project was designed as a randomized clinical trial to assess the effectiveness and safety of hybrid cardiac rehabilitation (HCR)—a combination of hospital-based cardiac rehabilitation (1 month) with a new form of home-based telemonitored cardiac rehabilitation (2 months) in HCM patients without left ventricular (LV) outflow tract obstruction and preserved systolic function. Sixty patients who fulfil the inclusion criteria have been randomly assigned (1:1) to either HCR plus usual care (training group) or usual care only (control group). The primary endpoint is a functional capacity evaluated by peak oxygen uptake (pVO2). Secondary endpoints include workload time during the cardiopulmonary exercise testing, a six-minute walk test distance, NT-pro BNP level, echocardiographic parameters of the left ventricular diastolic function (E/A, E/e’, myocardial strain rate), right ventricular systolic pressure, a gradient in the LV outflow tract, and quality of life. The tertiary analysis includes safety, acceptance and adherence to the HCR program. Our research will provide innovative data on the effectiveness and safety of hybrid cardiac rehabilitation in HCM patients without LV outflow tract obstruction and preserved systolic function. Clinical trials registry: ClinicalTrials.gov Identifier NCT03178357.