Introduction: Beside positive effects on athlete's health, competitive sport can be linked with an increased risk of illness and injury. Because of high relative increases in training, additional physical and psychological strains, and an earlier specialization and professionalization, adolescent athletes needs an increased attention. Training can alter the immune system by inducing a temporary immunosuppression, finally developing infection symptoms. Previous studies identified Epstein Barr Virus (EBV) as potential indicator for the immune status. In addition to the identification of triggering risk factors for recurrent infections, the aim was to determine the interaction between training load, stress sense, immunological parameters, and clinical symptoms. Methods: A controlled, prospective, longitudinal study on young athletes (n = 274, mean age: 13.8 ± 1.5 yrs) was conducted between 2010 and 2014. Also 285 controls (students, who did not perform competitive sports, mean age: 14.5 ± 1.9 yrs) were recruited. Athletes were examined 3 times each year to determine the effects of stress factors (training load: training hours per week [Th/w]) on selected outcome parameters (clinical [susceptibility to infection, WURSS-21: 21-item Wisconsin Upper Respiratory Symptom Survey], immunological, psychological end points). As part of each visit, EBV serostatus and EBV-specific IgG tiers were studied longitudinally as potential immune markers. Results: Athletes (A) trained 14.9 ± 5.6 h weekly. Controls (C) showed no lower stress levels compared to athletes (p = 0.387). Twelve percent of athletes reported recurrent infections (C: 8.5%, p = 0.153), the presence of an upper respiratory tract infection (URTI) was achieved in 30.7%. EBV seroprevalence of athletes was 60.3% (C: 56.6%, p = 0.339). Mean EBV-specific IgG titer of athletes was 166 ± 115 U/ml (C: 137 ± 112 U/ml, p = 0.030). With increasing Th/w, higher stress levels were observed (p < 0.001). Analyzes of WURSS-21 data revealed no relationship to training load (p = 0.323). Also, training load had no relation to EBV serostatus (p = 0.057) or the level of EBV-specific IgG titers (p = 0.364). Discussion: Young elite athletes showed no increased sense of stress, no higher prevalence of recurrent infections, and no different EBV-specific serological parameters compared to controls. Also, no direct relationship between training loads, clinical complaints, and EBV-specific immune responses was found. With increasing training loads athletes felt more stressed, but significant associations to EBV-specific serological parameters were absent. In summary, EBV serostatus and EBV-specific IgG titers do not allow risk stratification for impaired health. Further investigations are needed to identify additional risk factors and immune markers, with the aim to avoid inappropriate strains by early detection and following intervention.