This study focused on the differential expression levels of proteins that may exist between bone-derived and marrow-derived vascular endothelial cells (BVEC and MVEC). The vascular cells were isolated from trabecular bone regions and central marrow cavity regions of mouse long bones. Cells were cultured for 1 week to expand the population then separated from non-vascular cells using biotinylated isolectin B4, streptavidin-coated metallic microbeads, and a magnetic column. After an additional week of culture time, RNA was isolated from both cell types and compared using microarray analysis. RT-PCR was used to confirm and relatively quantitate the RNA messages. The bone-derived cells expressed more aldehyde dehydrogenase 3A1 (ALDH3A1), Secreted Modular Calcium-2 (SMOC-2), CCAAT enhancer binding protein (C/EBP-β), matrix metalloproteinase 13 (MMP-13), and annexin 8 (ANX8) than the marrow-derived cells. Spα and matrix GLA-protein (MGP) were produced in greater abundance by the marrow-derived cells. This study reveals that there are profound and unique differences between the vasculature of the metaphysis as compared to that of the central marrow cavity. The unique array of proteins expressed by the bone-derived endothelial cells may support growth of tumors from cancer cells that frequently metastasize and lodge in the trabecular bone regions. J. Cell. Biochem. 102: 463–472, 2007. © 2007 Wiley-Liss, Inc.