Early adverse experiences can precede long-term negative effects on physical health. Children experiencing armed conflict, flight and displacement, and refugee life may be at enhanced risk. Recent psychobiological models integrating knowledge about perinatal and childhood stress with susceptibility to chronic illnesses in later life make clear the pressing need for protective provision for war-affected children, who experience multiple traumas and continuing stressors. There is increasing recognition of the mechanisms linking physical and mental health with adult diseases seen as developmental disorders with origins early in life. Biological embedding models propose links between early adversity and increased vulnerability to later disease and premature death. Threat is central for children and families whose lives are changed by war and displacement, and may activate biological and behavioural systems that could increase the risk of long-term ill-health. Applying these models to understanding the experiences of refugees and the translation of these into the care provided and ways of monitoring and protecting long-term population health could potentially promote interventions to reduce longer term and secondary harms.