Recent advances in the study of andrology are unfolding some of the idiopathic components of male factor infertility. The inclusion of exercise training as a component of male factor infertility has been proposed secondary to changes observed in the reproductive hormone and semen profile of some endurance trained male athletes. Evidence exists that a subset of endurance trained men, particularly runners, present with subclinical changes in their reproductive hormone profile. These changes include a reduction in total and free testosterone, alterations in luteinising hormone release and alterations in pituitary responses to gonadotrophin-releasing hormone and other pharmacological perturbations. Less attention has been directed towards identifying changes in spermatogenesis and fertility capacity as a result of endurance training. The semen ejaculate of some endurance trained athletes presents with nonspecific modifications including a low normal sperm count, decreased motility and several morphological changes that may compromise fertility. Thus, although a subset of high mileage endurance trained runners present with subclinical modifications in their reproductive hormone and semen profile, to date there is no evidence that endurance training causes male infertility. Future investigations should focus on the clinical impact these hormone and semen alterations may have on fertility capacity in endurance trained athletes.