The number of women of all ages participating in physical activity is consistently increasing. Although there are numerous benefits to physical activity, specific problems may occur along the various stages of the female athlete's life, which need special attention. A remarkably late menarche, exaggerated beyond the expected genetic predisposition and a high prevalence of abnormal or absent menstrual cycles is seen in athletes, especially in dancers and long distance runners. Reproductive system dysfunction is associated with multiple factors, of which nutritional intake and caloric balance seem to be of a special importance. A high proportion of athletes suffer from pathological eating behaviours and there is an overlap between many features of anorexic patients and highly active athletes. The pathophysiology seen in most cases is hypo-oestrogenism due to suppression of the GnRH pulse generator. The mechanism(s) causing this reversible hypothalamic dysfunction are yet unknown. Of major concern are the skeletal abnormalities, including failure to reach peak bone mass, reduced bone density, scoliosis and stress fractures as a result of prolonged hypo-oestrogenism. Hormone replacement may be indicated in cases in which reduction of exercise or weight gain is not feasible or unsuccessful. Other populations that need special precautions are pregnant athletes and older women.