The prevalence of obesity, sarcopenia and osteoporosis is rising and there is increasing interest in determinants operating in early life. Fetal programming is the phenomenon whereby alterations in fetal growth and development in response to the prenatal environment have long term or permanent effects. Evidence for fetal programming of body composition and musculoskeletal development comes from epidemiological studies, investigation of the role of early undernutrition and preliminary findings on underlying mechanisms. Low birth weight and poor prenatal nutrition are associated with changes in adult body composition including altered fat distribution, reduced muscle mass and strength, and low bone mineral content. The mechanisms include a direct effect on cell number, altered stem cell function and resetting of regulatory hormonal axes. The next stage is translation of these findings into testable preventive strategies to maintain optimum body composition and minimize the risk of obesity, sarcopenia and osteoporosis in later life.