The aim was to evaluate the serum leptin level in children with protein-energy malnutrition (PEM) with and without pneumonia. The study included 60 children; 20 were controls, 20 had PEM without infection and 20 had PEM and pneumonia. They were subjected to nutritional assessments; serum leptin level, haemoglobin concentration, white-blood cell (WBC) count, CD4%, serum albumin, blood glucose, blood urea-nitrogen, and serum ferritin, and chest x-ray. Serum leptin levels were independently associated with pneumonia on multivariate analysis. In addition, serum leptin level and CD4% were significantly lower in the groups with PEM and pneumonia than in the group with PEM without pneumonia (p < 0.001). Low serum leptin levels were associated with pneumonia in children with protein energy malnutrition.