This review evaluates the status of the evidence that exercise training affects the menstrual cycle beginning with evidence for the existence of delayed menarche, amenorrhea, and luteal suppression in athletes. A later age of menarche and a higher prevalence of amenorrhea and luteal suppression have been observed in athletes, but there is no experimental evidence that athletic training delays menarche, and alternative sociological and statistical explanations for delayed menarche have been offered. Cross-sectional studies of amenorrheic athletes have revealed abnormal reproductive hormone patterns, suggesting that the GnRH pulse generator in the hypothalamus is failing to initiate normal hypothalamic-pituitary-ovarian function. Longitudinal data show that the abrupt initiation of a high volume of aerobic training can disrupt the menstrual cycle in at least some women, but these women may be more susceptible to reproductive disruption than others, and some aspect of athletic training other than exercise (such as caloric deficiency) may be responsible for the observed disruption. Luteal suppression may be an intermediate condition between menstrual regularity and amenorrhea in athletes, or it may be the endpoint of a successful acclimation to exercise training. A potential endocrine mechanism of menstrual disruption in athletes involving the hypothalamic-pituitary-adrenal axis is discussed. Finally, promising future directions for research on this topic are described.