Lung puncture aspirates were obtained from 99 malnourished children aged 9 months to 5 years with pneumonia, in order to identify the causative bacterial agents. Klebsiella species, Staphylococcus aureus and Escherichia coli were identified in 39.4%, 30.3% and 8.8% of aspirates, respectively. Approximately half to two-thirds of the children in each aetiological group had the same organisms isolated in both lung aspirates and blood. The bacterial agents reflected the immunocompromised status of the patients. Isolation of Klebsiella species was associated with age (p < 0.01), and type of malnutrition (p < 0.05); while that of Staphylococcus aureus was only statistically associated with type of malnutrition (p < 0.01). Gentamicin and cloxacillin represent a safe antibiotic regime for pneumonia in children with moderate to severe malnutrition.