A full genomic DNA microarray technique was employed to investigate the effects of Dongchunghacho on aortal and hepatic gene expression in apolipoprotein E knockout mice fed a high-fat/high-cholesterol diet. Male 8- week - old ApoE-/- mice were randomly divided into two groups, control(high cholesterol group; HC) and supplementation of Dongchunghacho (SD). All of the mice were fed a high-fet/high cholesterol diet with or without Dongchunghacho supplemented by 1% for 6 weeks. At first, lipid profile of the Dongchunghacho was measured by biochemical analysis. No differences were observed in serum triglyceride and total cholesterol levels between the two groups. Antigenotoxic effect of the Dongchunghacho was measured by the single cell gel electrophoresis assay (Comet assay) and quantified as % fluorescence in tail. Dongchunghacho supplementation decreased significantly leukocytic DNA damage and also there was a tendency of reduction in hepatic DNA damage in Dongchunghacho group compared with the control group. In up regulated genes in liver and aorta of the mice, genes with 0 to 2- fold difference in expression level between the two group (HD and SD) was very much more in liver than in aorta, on the contrary, those with 2-fold to 16-flod difference increased greatly rather in aorta than in liver. Also, almost the same results were observed in down regulated genes in liver and aorta between the two groups. These results suggested that supplementation of Dongchunghacho might be helpful in preventing leukocytic DNA damage induced by high fat diet, and has a more crucial roles in aortal gene expression.