Background: Racial immuno-haematological differences have been reported in children but to date have not been well quantified. Aim: To investigate differences in haemato-immunological markers over age between children born and living in Europe and Uganda. Subjects: HIV-uninfected children living in Uganda (n=1633) with cross-sectional data. Black (n=604) and white children (n=1355) living in Europe, both with prospective data. The children born in Europe were HIV-uninfected but born to HIV-infected mothers and were included in the European Collaborative Study (ECS). Methods: Patterns and levels of total lymphocyte (TLC), CD4+, CD8+ counts and CD4% were visualised by smoothers (a line representing the weighted average of all measurements over age by study group). Differences between groups were quantified using age-standardised Z-scores for individual TLC, CD4+ and CD8+ counts in uni- and multivariate regression models. Results: In infancy, TLC, CD4+ and CD8+ counts were lower in Ugandan than black European children; neutrophil counts were similar. Thereafter, only neutrophil counts were lower in Ugandan children. To assess within-race differences, we compared Z-scores of ECS children born to Ugandan mothers with those of Ugandan children. Levels of all four markers were lower in Ugandan children at all ages. In Ugandan children, CD4+ counts were 0.5985 Z-score (p<0.001) and neutrophil counts 0.3872 Z-score (p<0.001) lower than in European children born to Ugandan mothers. Conclusions: There are differences in levels of haemato-immunological markers in children with comparable genetic backgrounds, suggesting that environmental factors such as nutrition and exposure to micro-organisms might have important effects on the developing immune system. © 2006 The Liverpool School of Tropical Medicine.