Exercise represents a physical stress that challenges homeostasis. In response to this stressor, autonomic nervous system and the hypothalamic-pituitary-adrenal axis are known to react and to participate in the maintenance of homeostasis. This includes elevation of cortisol and cathecholamines in plasma. However, sustained physical conditioning in highly trained athletes is associated with a decreased hypothalamic-pituitary-adrenal response to exercise. On the other hand, highly trained athletes exhibit a chronic mild hypercortisolism at baseline that may be an adaptive change to chronic exercise. In addition the proinflammatory cytokine IL-6 is also activated. Moreover, exercise stimulates the secretion of GH and prolactin, and may influence the type of immunity by stimulating TH2 response profile. Besides, the stress of exercise inhibits the gonadal function, through the production of glucocorticoids and cathecholamines, as well as through activation of the CRH neurons. Nowadays, apart from the beneficial effects of exercise, there is increasing incidence of exercise-related short- and long- term consequences, especially concerning the female athlete that many authors describe as the so-called "exercise-related female reproductive dysfunction". These consequences include amenorrhea, infertility, eating disorders, osteoporosis, coronary heart disease and euthyroid "sick" syndrome. The mechanisms involved in the pathogenesis of the above disorders are discussed in this review.