In premenopausal women, the most severe menstrual dysfunction is amenorrhoea, which is associated with chronic hypoestrogenism. In postmenopausal women, hypoestrogenism is associated with a number of clinical sequelae related to cardiovascular health. A cardioprotective effect of endogenous oestrogen is widely supported, yet recent studies demonstrate a deleterious effect of hormone replacement therapy for cardiovascular health. What remain less clear are the implications of persistently low oestrogen levels in much younger amenorrhoeic athletes. The incidence of amenorrhoea among athletes is much greater than that observed among sedentary women. Recent data in amenorrhoeic athletes demonstrate impaired endothelial function, elevated low- and high-density lipoprotein levels, reduced circulating nitrates and nitrites, and increased susceptibility to lipid peroxidation. Predictive serum markers of cardiovascular health, such as homocysteine and C-reactive protein, have not yet been assessed in amenorrhoeic athletes, but are reportedly elevated in postmenopausal women. The independent and combined effects of chronic hypoestrogenism and exercise, together with subclinical dietary behaviours typically observed in amenorrhoeic athletes, warrants closer examination. Although no longitudinal studies exist, the altered vascular health outcomes reported in amenorrhoeic athletes are suggestive of increased risk for premature cardiovascular disease. Future research should focus on the presentation and progression of these adverse cardiovascular parameters in physically active women and athletes with hypoestrogenism to determine their effects on long-term health.