Abstract Background: Accurate and timely data on the health of a population are key for evidence-based decision making at both the policy and programmatic levels. In many low-income settings, such data are unavailable or outdated. Using an electronic medical records system, we determined the association between nutritional status and severe illness and mortality among young children presenting to a rural primary health care facility in the Gambia. Methods: Clinical data collected over five years (2010-2014) on children aged under 60 months making acute visits to a primary health care clinic in the rural Gambian district of Kiang West were retrospectively extracted from the medical records system. Generalised estimating equation models were used to investigate associations between nutritional status and illness severity, accounting for repeat visits, gender, age and access to transport to the clinic. The Population Attributable Fraction (PAF) was used to determine the proportion of severe illness likely attributable to different grades of malnutrition. Results: 3839/5021 (77%) children under 60 months of age living in Kiang West presented acutely to the clinic at least once, yielding 21,278 visits (47% girls, median age 20.2 months (Interquartile Range (IQR) 23.92 months)) and 26,001 diagnoses, 86% being infectious diseases. Severe illness was seen in 4.5% of visits (961/21,278). Wasting was associated with an increased risk of severe illness in a dose-dependent manner, (‘WHZ <-1’ adjusted Odds Ratio (aOR) 1.68, 95% CI:1.43-1.98, p<0.001, ‘WHZ <-2 and -3’ aOR 2.78, 95% CI:2.31-3.36, p<0.001 and ‘WHZ <-3’ aOR 7.82, 95% CI:6.40-9.55, p<0.001) the PAF for wasting (WHZ<-2) was 0.21 (95% CI: 0.18-0.24). Stunting, even in the most severe form (HAZ <-3), was not significantly associated with severe illness (aOR 1.19 95% CI:0.94-1.51) but was associated with a significantly increased risk of death (aOR 6.04 95% CI:1.94-18.78) Conclusion: In this population-based cohort of young children in rural Gambia, wasting was associated with disease severity in a dose-dependent manner. Further research is needed into strategies to identify and reach these children with effective interventions to improve their nutritional status.