Many studies of the endothelium have assumed equivalence between cultured confluent cells and an endothelial lining in vivo. We compared gene expression of bovine aortic endothelial cells (BAECsJ in culture versus freshly isolated cells from bovine aortas. Our technique of harvesting in vivo tissue yielded cells that were endothelial by the criteria of their containing von Willebrand factor (vWF) and lacking smooth muscle ar-actin, by both immunocytochemistry and tnRNA analyses. We found that several genes are overexpressed when BAECs are placed into culture, including basic fibroblast growth factor, platelet-derived growth factor B-chain, and thrombospondin. On the other hand, message for vWF is highly expressed in vivo and at lower levels in confluent cultures. The transcripts for transforming growth factor-/}, plakoglobin,and Jig (fins-likegene, FGF receptor-1) are comparable in vitro and in vivo. These results demonstrate that significant changes in gene expression occur in the transition from in vivo conditions to tissue culture of endothelial cells. Studies of in vitro endothelium may poorly reflect a quiescent endothelial lining in vivo but may be more similar to cells responding to injury or angiogenic stimuli.