Background: Intensive, prolonged endurance and strength training in apparently healthy young athletes causes many physiologic and structural adjustments in the heart, known as athlete’s heart. The correct distinction between physiological adaptations and pathological changes is crucial for the athlete, therefore screening programs are recommended by medical and sports associations. Nevertheless, a small but not negligible proportion of young competitive athletes die by sudden death. In 25% the cause of sudden cardiac death is genetic. Determining the genetic component is of key importance for distinction between athlete’s heart and cardiomyopathy. Methods: A gene panel next-generation sequencing (NGS) was performed in 41 apparently healthy young athletes without previously known heart disease. Results: Across 174 genes with known associations to different cardiac conditions, we identified nine variants: two pathogenic (P) variants and seven variants of unknown significance (VUSs). For all of them a more detailed follow-up with a cardiologist was advised. Conclusions: The results in our study suggest that targeted sequencing of genes associated with cardiovascular disease is the key that enables correct differentiation between athlete’s heart and cardiomyopathy, leading to fast and accurate clinical intervention where necessary. In this way, initial pathological changes are not confused with physiological ones, which could be fatal for the athlete if they continue with competitive sport.