The present study was performed to clarify of training-related modulations of the cardiopulmonary system (CPS) response sensitivity to a hypoxic and hypercapnia stimulus in young endurance athletes. The practical objective was to estimate a possible association between the reduction in sensitivity to respiratory homeostasis shifts and young athletes’ early sports specialization. Twenty-eight young male athletes aged 12.4–17.5 years with experience of strenuous endurance training in kayaking served as the subjects. The impact of strenuous endurance training was estimated in three parts of studies with athletes divided into age groups. Studies have demonstrated that endurance training in kayaking results in a distinct decrease in the CPS response sensitivity to hypoxia in young athletes. The responses to hypoxia in elite 16-year-old athletes do not significantly differ vs. elite adult athletes. Respiratory responses to hypercapnia also decreased (although to a lesser extent). Hypercapnic sensitivity in 16.3 yrs. do not significantly differ vs. elite adult athletes. When the responses were normalized to body mass, body surface and vital capacity, such differences were reliable. Chemo sensitivity CPS of young elite kayakers in 16.3 yrs. was significantly lower than in 14.9 yrs. The most expressed changes of respiratory responsiveness were noted in the response output during standard levels of hypercapnia and hypoxia. The greatest differences between young and adult elite athletes were revealed in hypercapnic ventilatory response. It is possible to believe that monitoring sensitivity and kinetic features of CPS responses in long-lasting high intensity of endurance training may be a prerequisite of best stimulation of its morphological and functional improvement. It can be assumed that the decrease in the CPS response sensitivity to the combined hypoxic and hypercapnic stimuli at long-lasting heavy kayaking training may deviate from the optimal one. In young kayakers it may be linked with trainability decline. But special studies need to confirm this assumption.