The purpose of this study was to investigate the effects of ovarian hormones on gene expression in the vascular wall. Our approach employed an RT-PCR-based cloning strategy of DNA differential display analysis, and verification/confirmation of differential expression by semi-quantitative PCR and real time PCR. mRNa analysis of normal aortas from intact and ovariectomized female C57BL/6J mice, showed altered expression of 20 genes with significant (> 70 %) sequence homology to known genes. Eight were selected for further study based on the genes' known function and potential relevance to vascular physiology. Differential expression of mRNA for three genes was confirmed by both semi-quantitative and real time RT-PCR using gene-specific primers. Ovariectomy downregulated expression of: elongation factor 1-alpha (3.5-fold), ganglioside-induced differentiation associated protein (8.2-fold), and NADH-ubiquinone oxidoreductase (3.8-fold). Thus, in normal mouse aortas ovariectomy resulted in significant differential down-regulation of a number of vascular genes important to vascular cell growth and angiogenesis, cellular differentiation, and mitochondrial energy metabolism, respectively. These studies have implications for our understanding of hormonal regulation of vascular gene expression, and the therapeutic targeting of specific vascular genetic sequences by female sex steroid hormones.