We have used microarrays to identify genes that are selectively expressed in endothelial cells in vivo. Analysis of freshly isolated endothelial cells from the lungs and kidneys reveals that 350 out of the 10,000 genes represented on the microarrays were expressed at higher levels than by the corresponding parenchymal cells. Thirteen of these genes were identified both in the lung and kidney screens from a subset of about 5000 genes. Many of these genes are known to be specifically expressed in endothelial cells, but about 200 genes were potentially novel endothelial genes. The preferential endothelial expression of a selected group of these genes was confirmed by quantitative polymerase chain reaction or in situ mRNA hybridization. Comparison of the genes expressed in lung and kidney endothelia revealed numerous differences. Notably, genes encoding components of an ephrin signaling pathway were highly expressed in lung endothelial cells. In summary, the genes we have identified represent potentially new pan-endothelial and tissue-specific endothelial markers.