BackgroundBloodstream infection (BSI) caused byKlebsiella pneumoniae(KP), is a leading cause of hospital-associated childhood mortality. There are limited data on how poor outcomes of KPBSI can be predicted in poorly resourced areas. This study aimed to assess if the profile of differential counts from full blood counts (FBC) taken at two time points in children with KPBSI could be used to predict the risk of death.MethodsWe conducted a retrospective study of a cohort of children admitted to hospital between 2006 and 2011 with KPBSI. FBC collected within 48 h (T1) of blood culture and 5–14 days later (T2), were reviewed. Differential counts were classified as abnormal if they were higher or lower than laboratory ranges for normal results. The risk of death was assessed for each category of differential counts. Risk ratios adjusted (aRR) for potential confounders were used to estimate the effect of cell counts on risk of death using multivariable analysis. Data were stratified by HIV status.ResultsOf 296 children, median age 5 (IQR:2–13) months, 82 were HIV -infected. Ninety-five (32%) children with KPBSI died. Mortality in HIV-infected and uninfected children was 39/82 (48%) and 56/214 (26%), respectively (p < 0.001). Independent associations with mortality were observed with leucopenia, neutropenia and thrombocytopenia. Risk of mortality in HIV-uninfected children with thrombocytopenia at T1 and T2 was aRR 2.5 (95% CI: 1.34–4.64) and 3.18 (95% CI: 1.31–7.73) respectively, whereas the mortality risk in the HIV-infected group with thrombocytopaenia at T1 and T2 was aRR 1.99 (95% CI: 0.94–4.19) and 2.01 (95% CI: 0.65–5.99) respectively. Neutropenia in the HIV-uninfected group at T1 and T2, showed aRR 2.17 (95% CI: 1.22–3.88) and aRR 3.70 (95% CI 1.30-10.51) respectively, while in the HIV-infected group, they were aRR 1.18 (95% CI 0.69–2.03) and aRR 2.05 (95% CI 0.87–4.85) at similar time points. Leucopenia at T2 was associated with mortality in HIV-uninfected and HIV-infected patients, aRR 3.22 (95%CI 1.22–8.51) and aRR 2.34 (95% CI 1.09–5.04) respectively. Persistent high band cell percentage at T2 in HIV-infected children indicated a risk of mortality of aRR 2.91 (95% CI 1.20–7.06).ConclusionAbnormal neutrophil counts and thrombocytopenia are independently associated with mortality in children with KPBSI. In resource-limited countries haematological markers have the potential to predict KPBSI mortality.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12887-023-04104-z.