Background Despite malaria, malnutrition and anaemia being major public-health challenges in Cameroon, very little has been reported on the interaction between these interconnected health determinants. This study therefore sought to investigate the relationship between malaria, anaemia, nutritional and socio-economic status amongst under—ten children living in six localities within two health districts in the North Region of Cameroon. Methods Accordingly, a cross- sectional survey was conducted during the peak malaria season in November 2014, in Pitoa and Mayo-Oulo Health Districts. Three hundred and sixty eight children aged 6months—10 years were enrolled. Structured questionnaires were used to assess socio-economic status. Anthropometric indices were taken using standard methods and nutritional status assessed by calculating Height for Age (HA), Weight for Age (WA) and Weight for Height (WH) z-scores to determine stunting, underweight and wasting respectively. Finger-prick blood samples were used to prepare thin and thick blood smears for microscopy. Whole blood was collected to determine the PCV and blood spots on filter paper were used to extract plasmodium DNA for speciation by PCR. Results Overall prevalence rates of malaria, malnutrition and anaemia were 32.9%, 54.1% and 20.6% respectively. Stunting, underweight and wasting were detected in 56.9%, 63.5% and 34.8% of the children respectively. There was a significant association between malaria and malnutrition [OR = 1.89, (95% CI: 1.12–3.19); (p = 0.017)]. Malnutrition was also strongly associated with malaria status [OR = 2.07, (95% CI: 1.22–3.53); (p = 0.007)]. The prevalence rates of mild, moderate and severe anaemia were 8.1%, 9.2% and 3.3% respectively. Both malaria status and anaemia correlated with development index [OR = 0.75, (95% CI: 0.58–0.99); (p = 0.042)] and [OR = 1.45, (95% CI: 1.05–2.00); (p = 0.023)] respectively. Conclusion Our findings show a synergistic relationship between malaria and malnutrition. Effective collaboration between malaria control and nutrition intervention programmes is essential for proper case management and improved socio-economic status.

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