We present the case of a 12-year-old boy with acute lymphocytic leukemia who developed pneumonia and multiple brain infarcts compatible with acute necrotic encephalitis. The infectious disease screening tests revealed influenza A H1N1 virus, Staphylococcus aureus in broncho alveolar lavage, E. coli and galactomannan antigen in blood. CNS influenza associated complications are reviewed. This case highlights the importance of magnetic resonance imaging as a diagnostic tool in the assessment of immunocompromised patients with CNS compromise and the value of brain biopsy in the final identification of an infectious disease etiology.