Background: Hyponatremia is the most common electrolyte imbalance encountered in the management of diarrheal children. Common ramifications include cerebral edema and fatal outcomes. However, pediatric data remain lacking, particularly in developmental contexts where resources are limited and associated conditions like malnutrition and pneumonia are common. Aim: This study aimed to evaluate predicting factors associated with hyponatremia in children under five years of age with severe acute malnutrition (SAM) in Bangladesh. Methods: Using a nested case-control design, we compared clinical and laboratory characteristics of children with (n = 61) and without hyponatremia (n = 183) taken from a parent population of all children under five with SAM and clinical or radiological pneumonia admitted to Dhaka Hospital of icddr,b between April 2011 and June 2012 (n = 407). Results: Logistic regression analysis adjusting for potential confounders such as lack of breast feeding, duration of vomiting (days), and severe wasting revealed that older age (OR 1.05, 95%CI 1.02 - 1.07, p = 0.001) (5% increase in the relative odds of hyponatremia for each additional month of age), presence of diarrhea (OR 2.43, 95%CI 1.0 - 6.0, p = 0.05), and difficulty breathing (OR 1.52, 95%CI 1.0 - 2.05, p = 0.05) were significantly associated with hyponatremia. Conclusion: Our data suggest that older age, presence of diarrhea, and difficulty breathing in under-five children with SAM is independent predictors of hyponatremia. These findings underscore the importance of detecting simple clinical predictors early in order to facilitate appropriate management and to prevent potential ramifications of hyponatremia in SAM children, especially in resource-poor settings.