Skeletal fragility associated with underlying childhood chronic disease is a systemic disorder of poor bone growth and reduction in bone turnover which can lead to abnormal bone mass, geometry and microarchitecture. Due to the growth potential unique to children, remarkable bone recovery following a transient threat to the bone can occur if there is concurrent growth. Addressing bone health in these children should focus on improvement in growth, puberty and removing the primary insult. In conditions where there is a little scope for bone recovery and limited residual growth, bone-targeted therapy may need to be considered, even though there is currently limited evidence. The importance of early detection of signs of bone fragility, by active screening for vertebral fracture using newer imaging techniques such as dual-energy X-ray absorptiometry lateral vertebral morphometry, may now be possible. There is currently, a paucity of evidence to support prophylactic use of anti-resorptive therapy. Where poor growth and low bone turnover are seen, the use of growth-promoting therapies and anabolic bone-protective agents may be more physiological and should be evaluated in well-designed trials. Collaborative studies on long-term fracture outcome and well-designed trials of bone-protective therapies are needed and to be encouraged.