Menstrual dysfunction is a common feature of all eating disorders and results in significant medical complications. The etiology of menstrual dysfunction is multifaceted and the result of a complex interplay of many factors including weight loss, decreased body fat, hypoleptinemia, abnormal eating attitudes and behaviors, exercise, and psychological stressors. This chapter will review the prevalence of menstrual dysfunction in adolescents with eating disorders, its multifactorial etiology, the evidence-based pathophysiology, and the resulting complications to linear growth, pubertal development, bone mineral accretion, and cognitive function. Future research directions are identified that suggest opportunities to gain new insights into our understanding of the mechanisms and treatment of menstrual dysfunction in adolescents with eating disorders.