For decades researchers reported that pre-menopausal women who engage in extensive endurance exercise and have menstrual dysfunction can develop low bone mineral density (BMD) or osteoporosis. More recently, low energy availability has been recognized as the initiating factor for low BMD in these women. Furthermore, the relationship between low energy availability and poor skeletal health is not exclusive to women engaging in endurance exercise. Rather, both males and females commonly experience endocrine dysfunction resulting from low energy availability and high exercise levels that degrades skeletal health. Consequences to skeletal health can range from short-term changes in bone metabolism and increased risk of bone stress injuries to long-term consequences of low BMD, such as osteoporosis and related fragility fractures. The degree to which low energy availability degrades skeletal health may be dependent on the length and extent of the energy deficit. However, the complex relationships between under-fueling, short- and long-term skeletal consequences and the factors that mediate these relationships are not well described. In this review, we discuss the consequences of low energy availability on sex hormones and skeletal health in two highly-active populations-athletes and military trainees-and provide a summary of existing knowledge gaps for future study.