The endocrine equilibrium which regulates reproductive function in women can be affected by physical and psychological factors. Blood levels of hormones depend on a balance between production, metabolism and clearance rates. Intensive physical exercise may affect this balance via different mechanisms, such as stress associated with competition, dieting, reduction of body fat and body weight, production of heat or hypoxia. Women who engage in regular high intensity exercise may be at risk, as a consequence of these hormonal changes, of developing menstrual disturbances such as oligomenorrhoea, delayed menarche and amenorrhoea. Impaired production of gonadotrophins, which leads to luteal phase deficiency and anovulation, is a common hormonal finding with exercise-induced menstrual disturbances, but several other hormones may show significant alterations. In this article we have reviewed the recent literature on the effects of intensive physical exercise on the menstrual cycle, on some important physical parameters such as bone mineral density and bodyweight, and on those hormones (gonadotrophins, prolactin, melatonin, opioid peptides and steroids) which regulate, directly or indirectly, the reproductive function in women.