The case of a 7 month-old baby boy is presented, with a history of several weeks of evolution of personality changes, convulsions and fever. While he was hospitalized, the brain image study showed multifocal cavity lesions, which varied from millimeters to 4 cm of diameter, not producing mass effect. Their biopsy revealed necrotizing encephalitis. In spite of treatment, the lesions progressed and the boy died. The autopsy demonstrated an extensive necrotizing encephalitis with fibrinoid necrotic arteritis, signs of organization, and the presence of parasitic elements with characteristics of trophozoites and cysts of free-living amoebas belonging to the genus Acanthamoeba or Balamuthia. In addition, hypoplasia-dysplasia of the thymus and signs of shock were found. The morphologic elements correspond to the disease described as granulomatous amebic encephalitis and the agent found was identified as Balamuthia mandrillaris (Centers for Diseases Control and Prevention, Atlanta, USA).