Female athletes are susceptible to both disordered eating and menstrual cycle disturbances (MCDs). Disordered eating in combination with high energy expenditure from exercise can lead to energy deprivation. Current theories suggest that MCDs are caused by energy deprivation rather than by exercise alone. A number of endocrine adaptations occur with energy deprivation and MCDs, which are concomitant with imbalanced bone turnover, reduced bone density and potentially increased fracture risk. This chapter reviews current evidence concerning the disruption of bone metabolism that accompanies disordered eating and MCDs in physically active girls and young women, including high-performance athletes. Initially, an overview of the aetiology of exercise-associated MCDs and their link with disordered eating is provided. Thereafter, studies reporting changes in areal bone mineral density (aBMD) in female athletes with MCDs are considered in conjunction with change in athletes' physical activity, nutritional status and menstrual histories. A comprehensive overview of the disruption of bone metabolism that accompanies nutritionally related MCDs is also provided. Emphasis is placed upon the role of energy deprivation and its endocrine effects, which, when sustained, result in imbalanced bone turnover and low aBMD. Based on current evidence, recommendations are made for the prevention and treatment of disturbed bone metabolism and low BMD in female athletes with MCDs. Finally, consideration is given to the effects of intense training and energy deprivation on endocrine function and skeletal health in men.