Caloric restriction caused by undernutrition or over-exercise is increasingly common and has significant health consequences such as hypothalamic amenorrhea, infertility, attainment of low peak bone mass, and bone loss leading to fracture. In these patients, the pathophysiology of amenorrhea and bone loss is multifactorial, involving hormones that integrate the nutritional state with the hypothalamic-pituitary-ovarian axis, including leptin and possibly ghrelin. The pathophysiology of bone loss includes nutritional deficiencies, possibly estrogen deficiency, and direct and indirect effects of leptin on bone. Identifying patients at risk for low bone mineral density and fracture is important, as is screening with dual energy radiograph absorptiometry. Treatment has focused on oral contraceptive use, yet improved bone mineral density is marked by nutritional recovery and anovulation reversal. Therefore, resolving the nutrition deficiency should be the cornerstone of treatment. Cognitive-behavioral therapy aims for weight recovery, which can lead to reversal of amenorrhea and improvement in other associated metabolic abnormalities. During treatment, estradiol levels can be followed to assess hypothalamic-pituitary-ovarian recovery because estradiol secretion may increase well before ovulation occurs. In patients failing the above interventions, hormone replacement should be considered, but bone mineral density should be followed because patients may continue to lose bone despite treatment with oral contraceptives if nutrition is not improved.