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Stenotrophomonas maltophila (S.maltophila) is an aerobic Gram-negative bacillus that is a frequent colonizer of fluids used in the hospital setting. The organism is known to cause life threatening infections in immuno-compromised patients especially in those who are neutropenic, on chemotherapy or on broad spectrum antibiotics. We report a case of ventilator associated pneumonia caused by Stenotrophomonas maltophila in a two-month old infant who later developed multi organ dysfunction syndrome. In seriously ill paediatric patients, S.maltophila should also be considered as a possible pathogen for Ventilator-Associated Pneumonia (VAP), hence empiric antibiotic choice should include antimicrobials that are active against S. maltophila. An early identification and treatment of VAP with Multi-Drug Resistant (MDR) strains with appropriate antibiotics has a significant impact on morbidity and mortality.