Purpose: The aim of this study was to investigate the structural and electrical changes in the heart associated with exercise in young athletes under 18 years of age and to examine the relationship between these changes and biochemical markers. Materials and Methods: In this study, 32 male paediatric athletes (five rowers, five kayakers and 22 footballers) were prospectively evaluated. Dynamic exercise training for 75 minutes was applied to all athletes. An echocardiographic evaluation was performed on the athletes at rest. An electrocardiogram (ECG) was taken before and after the exercise. Blood samples were taken from all athletes before the exercise, during the first hour of exercise and after the fourth hour of the training session to analyse the serum levels of creatine kinase myocardial band, troponin T(cTnT) and pro-brain natriuretic peptide. Results: The mean age of all athletes was 15.3±0.9 years. In the echocardiography examination, end-diastolic thickness, left ventricular end-diastolic diameter, posterior wall end-diastolic diameter, left ventricular end-systolic diameter, left ventricular mass measurements (LVM) and left ventricular mass indices (LVMI) were higher among the rowers than in the remaining groups. In the post-exercise ECG, T-wave peaks were observed in 16 individuals, including all rowers, all kayakers, and six footballers. The cTnT values in the first hour and after the fourth were 0.31–0.71 ng/ml in football players, 0.10–0.27 ng/ml in rowers, and 0.04–0.15 ng/ml kayakers. An increase in cTnT levels was detected after the fourth hour of exercise in all groups. There was a correlation between T-wave peaks in the ECG taken after exercise and age, cTnT serum level and increased LVM. Conclusion: In this study, we found T-wave peaks in half of the athletes after exercise. The serum cTnT levels of young athletes may be elevated by exercise and that LVM and LVMI may be higher in athletes. Echocardiography and ECG evaluations should be performed in paediatric athletes.