Fish oil and shortening have been suggested to have opposite effects on cardiovascular disease (CVD). This study investigated the effect of shortening and fish oil on CVD risk factors and aorta histopathology, and the association between risk factors and aorta histopathology. Male Wister rats (n=30) were fed an AIN-93G diet containing 20% fat in the form of fish oil, shortening, or soybean oil for 4 weeks. Total cholesterol (TC), triacylglyceride (TG), and C-reactive protein levels were significantly (P<0.001) lower in the fish oil than in soybean oil and shortening groups. HDL-cholesterol concentrations were significantly different (P<0.001) between groups. In addition, LDL-cholesterol levels were significantly (P<0.001) lower in the fish oil and shortening groups than in the soybean oil group. Insulin and glucose concentrations did not differ among groups. Effect of dietary fat on tissue fatty acid composition significantly differed in abdominal fat and brain compared with RBC, heart, kidney and liver. The aortic wall was significantly (P=0.02) thinner in the fish oil group than in the soybean oil and shortening groups. The aortic wall thickness was positively correlated with TG and TC, but negatively with EPA + DHA levels of all tissues. These results suggested that fish oil had protective effects on aorta histopathology by hypolipidemic action in this rat model.