Free-living amebae etiologically associated with central nervous system (CNS) infection in children have included Acanthamoeba, Naegleria, and recently, leptomyxid ameba. Two previously healthy children are reported with CNS infection caused by leptomyxid ameba, recently classified as Balamuthia mandrillaris. One child, a 27-month-old boy, had right hemiparesis and aphasia, and the other, a 13-year-old girl, had headache, right hemiparesis, diplopia, and left facial weakness. Cerebrospinal fluid studies of both children revealed a mononuclear pleocytosis and mildly elevated protein. The younger child developed seizures and progressive cerebrovascular occlusions; both developed hydrocephalus and coma progressing to death 16 days after onset of symptoms. The younger child at autopsy had necrotizing meningoencephalitis, left internal carotid arteritis, and amebic trophozoites and cysts in brain. Perivascular trophozoites were difficult to distinguish morphologically from macrophages in the older child, who had no cyst forms. Indirect immunofluorescence test revealed CNS infection with B. mandrillaris in both. This leptomyxid ameba, formerly considered an innocuous soil organism, should be considered in the differential diagnosis of progressive or atypical childhood stroke.