| Summary: | Abstract Background In malaria-endemic settings, a small proportion of children suffer repeated malaria infections, contributing to most of the malaria cases, yet underlying factors are not fully understood. This study was aimed to determine whether undernutrition predicts this over-dispersion of malaria infections in children aged 6–18 months in settings of high malaria and undernutrition prevalence. Methods Prospective cohort study, conducted in Mangochi, Malawi. Six-months-old infants were enrolled and had length-for-age z-scores (LAZ), weight-for-age z-scores (WAZ), and weight-for-length z-scores (WLZ) assessed. Data were collected for ‘presumed’, clinical, and rapid diagnostic test (RDT)-confirmed malaria until 18 months. Malaria microscopy was done at 6 and 18 months. Negative binomial regression was used for malaria incidence and modified Poisson regression for malaria prevalence. Results Of the 2723 children enrolled, 2561 (94%) had anthropometry and malaria data. The mean (standard deviation [SD]) of LAZ, WAZ, and WLZ at 6 months were − 1.4 (1.1), − 0.7 (1.2), and 0.3 (1.1), respectively. The mean (SD) incidences of ‘presumed’, clinical, and RDT-confirmed malaria from 6 to 18 months were: 1.1 (1.6), 0.4 (0.8), and 1.3 (2.0) episodes/year, respectively. Prevalence of malaria parasitaemia was 4.8% at 6 months and 9.6% at 18 months. Higher WLZ at 6 months was associated with lower prevalence of malaria parasitaemia at 18 months (prevalence ratio [PR] = 0.80, 95% confidence interval [CI] 0.67 to 0.94, p = 0.007), but not with incidences of ‘presumed’ malaria (incidence rate ratio [IRR] = 0.97, 95% CI 0.92 to 1.02, p = 0.190), clinical malaria (IRR = 1.03, 95% CI 0.94 to 1.12, p = 0.571), RDT-confirmed malaria (IRR = 1.00, 95% CI 0.94 to 1.06, p = 0.950). LAZ and WAZ at 6 months were not associated with malaria outcomes. Household assets, maternal education, and food insecurity were significantly associated with malaria. There were significant variations in hospital-diagnosed malaria by study site. Conclusion In children aged 6–18 months living in malaria-endemic settings, LAZ, WAZ, and WLZ do not predict malaria incidence. However, WLZ may be associated with prevalence of malaria. Socio-economic and micro-geographic factors may explain the variations in malaria, but these require further study. Trial registration NCT00945698. Registered July 24, 2009, https://clinicaltrials.gov/ct2/show/NCT00945698, NCT01239693. Registered Nov 11, 2010, https://clinicaltrials.gov/ct2/show/NCT01239693
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