BackgroundSevere anaemia is a major cause of hospital admission and mortality in children living in sub-Saharan Africa, but data on its association with invasive bacterial infection are sparse. We aimed to characterise severe anaemia and its association with invasive bacterial infection in Kenyan children.MethodsIn this retrospective observational study, we systematically collected admission data for children aged 1 month to 14 years admitted to Kilifi County Hospital, Kenya, between Aug 1, 1998, and July 31, 2024. We excluded children with missing haemoglobin data. We examined prevalence, trends, and factors associated with severe anaemia and very severe anaemia, and the association between severe or moderate anaemia and odds of bacteraemia. Anaemia severity was defined using WHO age-specific thresholds.FindingsOf the 84 348 admissions, representing 64 499 unique children (28 232 [43·8%] females and 36 265 [56·2%] males), included in our analysis, 16 715 (19·8%) admissions had severe anaemia. Severe anaemia was associated with multiple, co-occurring risk factors, including sickle cell disease, malaria, HIV, and malnutrition. As malaria transmission declined (2004-09), the age distribution of severe anaemia shifted towards older children; cases in children aged 5-14 years increased from 16·4% during the high-transmission era (1998-2003) to 44·7% during the low-transmission era (2010-24). Compared with mild or no anaemia, severe anaemia was associated with higher odds of in-hospital mortality (adjusted odds ratio 2·1 [95% CI 1·9-2·3]) and bacteraemia (2·7 [2·5-3·0]), particularly with non-typhoidal Salmonella (6·1 [4·6-8·1]), Escherichia coli (5·7 [4·2-7·7]), Haemophilus influenzae (4·3 [3·0-6·4]), Streptococcus pneumoniae (3·5 [2·9-4·2]), and Klebsiella pneumoniae (2·4 [1·4-4·0]). Moderate anaemia was also associated with increased odds of bacteraemia and mortality.InterpretationSevere anaemia in hospitalised Kenyan children is multifactorial, increasingly affects older children, and is strongly associated with pathogen-specific bacteraemia and increased mortality. These findings support prompt evaluation for bacteraemia and closer clinical management in severely anaemic children to improve survival.FundingWellcome and the Science for Africa Foundation to the DELTAS Africa programme.