The impact of coronavirus infection (SARS-CoV-2) on cardiac output in underage athletes is uncertain. The study was aimed to determine heart disease in young elite athletes having a history of COVID-19 (SARS-CoV-2). A retrospective analysis of the results of the developed three-phase medical assessment of 236 elite athletes aged 14–17 (16 ± 1), who had had SARS-CoV-2 infection, was performed. The first phase of assessment involved examination, ECG, ECHO, bicycle ergometry (BEM), creatine kinase and creatine kinase MB tests. During the second phase 22 athletes (9.3%) underwent a more thorough assessment that included Holter monitoring (HM) with heart rate turbulence (HRT), microvolt T–wave alternans (MTWA), heart rate variability (HRV) estimation, high-resolution ECG (HRECG), determination of myocardial damage biochemical markers (troponin, NТproBNP) due to alterations revealed. Seven athletes (32%) having alterations revealed during this phase were referred to gadolinium enhancement cardiac magnetic resonance imaging (MRI) (the third phase). Myopericarditis was diagnosed in four cases (1.7% of 236) based on the results. Thus, low (below 2%) myocardial involvement has been revealed in young elite athletes, who have a history of SARSCoV-2 infection. Cardiovascular assessment algorithm has been developed for such athletes. Detection of cardiac arrhythmias by ECG, BEM, and HM is the most informative. HRECG, HRV, HRT, and MTWA can be used as additional methods to determine indications for MRI as a gold standard of the diagnosis of myocarditis.