We sought to investigate right heart remodeling and function in elite athlees, as well as the relationship between parameters of right ventricular (RV) and right atrial (RA) remodeling and indices of aerobic capacity. Elite male athletes (n = 352) underwent echocardiographic examination including the evaluation of RV and RA parameters. Maximal cardiopulmonary exercise testing was performed to measure maximal oxygen consumption (VO_2max), ventilatory anaerobic threshold (VAT) and heart rate reserve (HRR). The right heart remodeling was different between groups. Soccer players had significantly higher RV and RA diameters indexed for BSA. RV filling pressure assessed by tricuspid E/e’ ratio was the lowest in soccer players, suggesting somewhat better RV diastolic function. Functional capacity also varies between groups of athletes. VO_2max was the highest among soccer players, somewhat lower in basketball players and and the lowest among water polo players (55.3 ± 5.6 vs. 52.1 ± 5.9 vs. 53.5 ± 4.8 ml/kg/min, p < 0.001). Age, average weekly duration of training, percentage of body fat, as well as parameters of cardiopulmonary fitness (VO_2max, O₂ pulse, HRR), correlated well with parameters of RV and RA structure and function in the whole study population. However, systolic blood pressure at rest, VO_2max and LV mass index are independently associated with RV and RA structure, whereas duration of training shows the best association with parameters of RV systolic and diastolic function. Even though soccer, water polo and basketball belong to the same group of sports, there is a significant difference in RV and RA remodeling between these three groups. It seems that right heart adaptation is the most pronounced in soccer players, who also have the highest maximal oxygen consumption. Further studies are necessary to investigate the mechanisms of these differences.