Objectives To develop a simple, accurate and reproducible method, which combines macro and histopathological techniques for determining the degree of lipid deposition in genetically modified mice. Method The entire aortas from C57BL / 6, ldlr- / - and apoE- / - mice were stained with Sudan Ⅳ using either in vivo perfusion or traditional in vitro enface staining techniques. Histological sections of aortic root and hearts were embedded in tissue freezing medium and cut with a cryostat, then stained with Oil Red O. The calculated aortic root area based on the aortic root circumference was used to reduce measurement errors. Results The in vitro en face staining can stain all fat, which include the adventitial tissue around aorta. However the in vivo perfusion staining can specifically stain the fatty deposition inside of aorta. Both entire aorta and aortic root section staining showed that there was a highly significant increase in fatty deposition in the aortas of the genetic modified mice. Although all mice genetic background was same, the apoE- / - mice had larger atherosclerotic lesions than ldlr- / - mice. Conclusions The new in vivo perfusion method is more accurate than the in vitro en face method. The combination of these macro and microscopic techniques overcomes the shortcomings of the earlier published methods which are generally limited to the measurement of fatty red staining areas only, neglecting non-specific adventitial fat staining around aorta and aortic root section tissue distortion. Objectives To develop a simple, accurate and reproducible method, which combines macro and histopathological techniques for determining the degree of lipid deposition in genetically modified mice. Method The entire aortas from C57BL / 6, ldlr- / - and apoE- / - mice were stained with Sudan IV using either in vivo perfusion or traditional in vitro enfinition staining techniques. Histological sections of aortic root and hearts were embedded in tissue freezing medium and cut with a cryostat, then stained with Oil Red O. The calculated aortic root area based on the Results The in vitro en face staining can stain all fat, which include the adventitial tissue around aorta. However the in vivo perfusion staining can specifically stain the fatty deposition inside of aorta. Both entire aorta and aortic root section staining showed that there was a highly significant increase in fatty deposition in the aortas of the genetic modified m ice. Although all mice genetic background was same, the apoE- / - mice had larger atherosclerotic lesions than ldlr- / - mice. Conclusions The new in vivo perfusion method is more accurate than the in vitro en face method. The combination of these macro and microscopic artwork overcomes the shortcomings of the earlier published methods which are generally limited to the measurement of fatty red staining areas only, neglecting non-specific adventitial fat staining around aorta and aortic root section tissue distortion.