Introduction: Heterozygous β-thalassaemia occurs at low frequency in coastal Kenya, but its clinical significance is poorly understood. While some evidence suggests protection against malaria, its influence on childhood health and survival in African children remains unknown. Methods We conducted the prospective analysis of a cohort of 15,077 children recruited at age 3–12 months of age (72 β-thalassaemia heterozygotes and 15,005 controls) and followed passively for disease-specific hospital admission and survival until their fifth birthday. Results β-thalassaemia heterozygotes were more frequently admitted than controls with severe (Hb <5g/dl) [adjusted Incidence Rate Ratio 5.1 (95% CI 1.3-20.0; P=0.02)] and moderate (Hb <10g/dl) anaemia [aIRR 2.3 (95% CI 1.3-3.9; P=0.004)]. No other significant differences were found. Conclusion Heterozygous β-thalassaemia increased the risk of anaemia-related hospital admissions within this cohort, highlighting the need to investigate the underlying triggers of anaemia in such children.