Background The balance between endothelial injury and repair in childhood is poorly understood. We examined this relationship in healthy children, in adults and in children with familial hypercholesterolaemia (FH). Methodology Circulating endothelial cells (CECs) were measured as a marker of vascular injury, with vascular repair assessed by counting colony forming units (CFUs), also known as endothelial progenitor cells. Results CEC number increased with age. Children with FH had elevated CECs compared to healthy children , with similar levels numerically to those found in healthy adults. CFU numbers were higher in healthy children than either healthy adults or children with FH. Endothelium dependent vascular function, measured by flow-mediated dilatation (FMD), was positively associated with CFU number, even following adjustment for confounding risk variables. Conclusion Levels of CECs increase and CFUs decrease with age. In childhood, before the onset of clinically detectable cardiovascular dysfunction, children with a major risk factor for atherosclerotic disease have levels of these indices of vascular injury and repair approaching those seen in adults.