Endothelial cells of blood vessels forming the interphase between systemic circulation and tissues are crucial for maintenance of homeostasis and organ-related functions. Recent experiments support organ-specific endothelial differentiation and suggest differential gene expression patterns in endothelial cells. Here, we compared gene expression in primary human cerebral endothelial cells (HCEC), which are major constituents of the blood brain barrier (BBB), with human umbilical vein endothelial cells (HUVEC) by using cDNA array analysis of 375 genes. Under basal culture conditions, 35 genes were expressed only in HCEC, whereas 20 gene transcripts were detected only in HUVEC. A total of 78 genes were expressed in both endothelial cell types partly with distinct expression levels. Genes expressed by cerebral endothelial cells are important in vasculo- and angiogenesis (VEGF, erbB1) and immunoregulation (OSM-Rbeta, decorin, IL-6) or have growth-supporting properties (brain-derived neurotrophic factor, stem cell factor, transforming growth factor-beta). The differential gene expression profiles were confirmed at the protein level of cell cultures (ELISA, immunoblotting) and human tissues (immunohistochemistry). Identification and further functional characterization of genes specifically expressed by cerebral endothelial cells will have important impact on our understanding of endothelial function at the BBB.