Cerebral malaria (CM) can be a fatal manifestation of Plasmodium falciparum infection. We examined global gene expression patterns during fatal murine CM (FMCM) and noncerebral malaria (NCM) by microarray analysis. There was differential expression of a number of genes, including some not yet characterized in the pathogenesis of FMCM. Some gene induction was observed during Plasmodium berghei infection regardless of the development of CM, and there was a predominance of genes linked to interferon responses, even in NCM. However, upon real-time PCR validation and quantitation, these genes were much more highly expressed in FMCM than in NCM. The observed changes included genes belonging to pathways such as interferon signaling, major histocompatibility complex processing and presentation, apoptosis, and immunomodulatory and antimicrobial processes. We further characterized differentially expressed genes by examining the cellular source of their expression as well as their temporal expression patterns during the course of malaria infection. These data identify a number of novel genes that represent interesting candidates for further investigation in FMCM.Malaria is a devastating disease affecting developing countries in the tropical and subtropical regions of the world. Cerebral malaria (CM), a severe manifestation of Plasmodium falciparum infection, can lead to neurological complications and death (64). Murine models of malaria are important tools for studying the pathogenesis of malaria, with numerous clinical and histopathological similarities between human and murine malaria having been described (19). Comparisons between fatal murine CM (FMCM) and noncerebral malaria (NCM) provide valuable insights into the pathogenesis of CM.A number of significant changes in the murine brain that characterize CM have been described, including breakdown of the blood-brain barrier (62), redistribution and activation of glia (31,32,34), apoptosis of endothelial cells and astrocytes (46,47), metabolic changes (44, 48), and distinct patterns of chemokine gene expression (38).A recent approach to identifying novel changes within the brain during CM is to profile gene expression changes using microarray technology (9, 30). Microarray studies can generate a plethora of data that pinpoint involvement of unknown or poorly characterized genes, stimulating investigation of their biological functions. Some studies have used microarrays to examine global gene expression patterns during murine malaria, defining gene expression profiles that are associated with susceptibility or resistance to murine CM (26, 27), identifying genes in the brain that discriminate between different outcomes of Plasmodium infection (5), or describing trends in gene expression within the brain (55). Studies on the spleen have been performed to find genes that differentiate between cerebral and noncerebral (55) and between lethal and nonlethal (52) forms of murine malaria. Microarrays also have been used to examine Plasmodium infection in humans (14, 41) and monke...