Phenylketonuria, galactosemia and celiac disease are disorders in which elimination diets are the only known therapy, which reverses many clinical manifestations of acute phase in the patients. Unfortunately, most of them develop long-term complications, including bone turnover impairment and low bone mineral density. These disturbances are not only observed in adulthood but also in childhood and adolescence. Insufficient accumulation of peak bone mass in these periods is a risk factor for osteoporosis and fractures in later life. The pathological mechanisms leading to a diminished bone mineral content in these disorders are not well known. The patients might be at risk for a decreased bone mineral content because of either dietary deficiencies secondary to the elimination diets and/or unknown intrinsic factors. This article overviews bone metabolism disturbances in phenylketonuria, galactosemia and celiac disease during childhood and adolescence, when growth and bone turnover are most intensive. The available data and own results concerning bone markers in children with these disorders and proposal for the prevention of osteoporosis in pediatric patients treated with elimination diets are discussed.