OBJECTIVES: To Understand the development of sporadic cerebral cavernous malformations (SCCM) comprehensively, we analyzed gene expression profiles in SCCMs by gene microarray. METHODS: The total number of the specimens collected in our study was 14, 7 of which were SCCMs, and the others were controls that were obtained from normal brain vessels. The total RNA was extracted and hybridized with oligonucleotide array containing 21522 genes. The analysis of Gene Ontology (GO) items and molecular pathways was performed based on the GO and Kyoto Encyclopedia of Genes and Genomes databases. The gene coexpression networks were constructed to identify the core genes regulating the progression of SCCMs. RESULTS: A total of 785 probes, showing differentially expressed genes (DEGs) between the 2 groups, were found by the gene chips. According to the analysis based on GO and Kyoto Encyclopedia of Genes and Genomes, 286 GO terms and 53 pathways were identified to be significantly relevant with the DEGs. All differential gene interactions were analyzed and the core genes were selected in the coexpression networks. CONCLUSIONS: The gene expression profiles obtained from SCCMs were significantly distinct from those of control brain vascular specimens. These DEGs are related to multiple molecular signal pathways, such as the mitogen-activated protein kinase pathway, cytokine-cytokine receptor interaction, focal adhesion, and inflammatory response. According to the analysis of the core genes selected in the gene coexpression networks, we postulated that CSF1R, XCL1, KCNMB1, RHOG, and TJP1 might exert enormous functions in the pathogenesis of SCCMs. However, further studies are required to aid in the clinical diagnosis and prevention of SCCMs.