The aim of this study was to evaluate endothelial function measured as flow-mediated dilatation (FMD) of the brachial artery and blood markers of cardiovascular disease in young female endurance athletes with menstrual disturbance. Age- and body mass index-matched groups of young endurance athletes with amenorrhea (n = 14), oligomenorrhea (n = 9), and regular cycles (n = 12) and sedentary controls (n = 12) were compared with respect to endothelial function, lipid profile, markers of inflammation, and endocrine status. We found a significantly decreased FMD in the amenorrheic athletes, compared with all other groups. Amenorrheic athletes also had the most unfavorable lipid profile with significantly higher total cholesterol and low-density lipoprotein, compared with the other athlete groups. The oligomenorrheic athletes had the lowest levels of total cholesterol, low-density lipoprotein, and apolipoprotein B of all groups and significantly lower in comparison with the amenorrheic group. However, with respect to FMD, the oligomenorrheic group represented an intermediate between amenorrheic and regularly cycling subjects. There was a gradual impairment of FMD and the lipid profile to the degree of menstrual disturbance supporting an association with estrogen status. We conclude that amenorrhea in young endurance athletes is associated with endothelial dysfunction and unfavorable lipid profile. Additional studies are needed to elucidate the clinical implications of these results with regard to long-term risk for cardiovascular disease.