Increased longevity and improved medical management of children with chronic illnesses has led to a focus on the short- and long-term consequences of these conditions on bone health. Bone loss is influenced by diet, malabsorption, and disease-related imbalances in bone turnover. It may be exacerbated by common medications, especially corticosteroids. Assessment of bone mass and quality, calcium absorption, kinetically derived rates of bone turnover, and biochemical markers of bone turnover have increased our knowledge of the pathophysiology of bone loss in these children as well as provided insights into possible therapeutic interventions. Increased intake of calcium and vitamin D, while useful, is unlikely to prevent or resolve bone loss in many chronically ill children. Emphasis on combination of nutritional interventions with exercise and newer bone-sparing therapies may be necessary.