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Background Exposure to adverse experiences during pregnancy, such as a natural disaster, can modify development of the child with potential long-term consequences. Elemental hair analysis may provide useful indicators of cellular homeostasis and child health. The present study investigated (1) if flood-induced prenatal maternal stress is associated with altered hair elemental profiles in 4-year-old children, and (2) if hair elemental profiles are associated with behavioural outcomes in children. Methods Participants were 75 children (39 boys; 36 girls) whose mothers were exposed to varying levels of stress due to a natural disaster (2011 Queensland Flood, Australia) during pregnancy. At 4 years of age, language development, attention and internalizing and externalizing problems were assessed and scalp hair was collected. Hair was analyzed by inductively coupled plasma mass spectrometry (ICP-MS) for 28 chemical elements. Results A significant curvilinear association was found between maternal objective hardship and copper levels in boys, as low and high maternal objective hardship levels were associated with the highest hair copper levels. Mediation analysis revealed that low levels of maternal objective hardship and high levels of copper were associated with lower vocabulary scores. Higher levels of maternal objective hardship were associated with higher magnesium levels, which in turn were associated with attention problems and aggression in boys. In girls, high and low maternal objective hardship levels were associated with high calcium/potassium ratios. Conclusion Elemental hair analysis may provide a sensitive biomonitoring tool for early identification of health risks in vulnerable children.