The recently introduced HCM-AF Risk Calculator allows the prognosis of atrial fibrillation (AF) occurrence in hypertrophic cardiomyopathy (HCM) patients. The aim of this study was to assess the clinical application of the HCM-AF Risk Score in the prediction of the clinical outcomes of Polish patients. The study included 92 patients (50.0% female, median age 55 years), with a baseline sinus rhythm diagnosed between 2013 and 2018. The analysis involved the incidence of clinical characteristics and outcomes, total mortality, rehospitalisation, and the course of heart failure (HF). According to the HCM-AF Risk Score, the HCM population was stratified into three subgroups, with a low (13/14.2%), intermediate (30/32.6%), and high risk of AF (49/53.2%). Subgroups differed significantly: the high-risk subgroup was older, had a higher body mass index (BMI), and more advanced signs of left ventricular (LV) hypertrophy and left atrium (LA) dilatation. The registered AF incidence was 31.5% and 43.5% in the 2- and 5-year follow-ups, and it was significantly higher than in the HCM-AF Risk Score population, which had 4.6% in the 2-year follow-up, and 10.7% in the 5-year follow-up. In the whole population, the AF incidence in both the 2- and 5-year follow-ups revealed a strong correlation with the HCM-AF Risk Score (r = 0.442,p< 0.001; r = 0.346,p< 0.001, respectively). The clinical outcomes differed among the subgroups: the total mortality was 15.4% vs. 20.0% vs. 42.9% (p< 0.05); rehospitalisation was 23.1% vs. 53.3% vs. 71.4% (p< 0.05). The highest HF progression was in the high-risk subgroup (36.7%). Regardless of the high results of the HCM-Risk Score in Polish patients, the score underestimates the real-life high level of AF incidence. The HCM-AF Risk Score seems to be useful in the prediction of the general clinical outcomes in HCM patients.