Von Willebrand factor (VWF) mediates the adhesion of platelets to sites of vascular injury and acts as a carrier for coagulation factor VIII. Qualitative or quantitative defects in VWF result in von Willebrand disease, the most common inherited bleeding disorder. VWF is a prototypical tissue-specific gene, with its expression limited to endothelial cells and megakaryocytes. Although in vitro studies have identified several important transcription factor binding sites near or within the VWF promoter, transgenic models carrying these sequences have failed to recapitulate fully the endogenous VWF expression pattern. Thus, it is likely that unidentified distant sequences are involved. To gain a better understanding of the cis-regulatory expression program for VWF and other endothelial-specific genes, we identified 262 conserved noncoding sequences (CNSs) located within the upstream intergenic region and first intron of 28 endothelial-specific genes. Thirty-three percent of the CNSs were DNase hypersensitive in endothelial cells, while only 16% were hypersensitive in control fibroblasts. We also searched for short sequence patterns overrepresented in the endothelial CNSs when compared to CNSs from control gene sets. One motif, SAGGAAR, was strongly overrepresented in endothelial CNSs. This motif corresponds to the binding site for members of the Ets family of transcription factors, several of which are already known to be involved in endothelial gene regulation. We also generated a set of transgenic mouse lines from overlapping BACs covering 362 kb of sequence around the murine Vwf locus. Two BACs showed lacZ reporter activity consistent with endogenous VWF expression in nearly all tissues tested. Our transgenic experiments suggest that distant sequences are required for the full Vwf gene expression program. These studies lay the foundation for the identification and testing of endothelial-specific regulatory elements, leading to a better understanding of the mechanisms involved in the control of tissue-specific gene regulation.