Background: Non-alcoholic fatty liver disease (NAFLD), an emerging public health problem, may be a highly atherogenic condition. But the relationship between fatty liver diseases and carotid atherosclerosis in small-animal is incompletely understood. The purpose of the present study was to evaluate carotid intima-media thickness (IMT) in NAFLD rats using high-frequency ultrasonic diagnostic equipment, and to ascertain if the degree of hepatic pathological changes was associated with carotid IMT. Results: Liver injury was induced by a high-fat diet for 8, 12 and 16 weeks, separately, in fifty four SD rats (27 treated, 27 controls). Liver echogenicity and IMT of the carotid and aorta were evaluated and compared to histological findings of them. In comparison with the rats in the control group, fatty liver disease in rats was characterized by homogeneous and diffusely increased echogenicity (bright liver), an increased anteroposterior diameter of the liver and serum biochemical changes. Hepatic histological analyses demonstrated indications of simple steatosis in rats induced by an 8-week high-fat diet, and a high-fat diet for 12 weeks and 16 weeks could induce steatohepatitis (NASH) in rats. The 12- and 16-week groups had a significantly higher inflammation scores than those of the control groups. IMT values for the carotid and aorta were remarkably increased in the NASH groups compared with the control groups (P < 0.05). The end-diastolic velocity and systolic peak velocity of the carotid and aorta in the NASH groups were significantly smaller than those in the control group. A significant correlation between the IMT of the carotid with hepatic inflammation score (r(2) = 0.598, P = 0.001) and the systolic peak velocity of the carotid (r(2) = -0.342, P = 0.041) were shown in NAFLD rats. Conclusion: We demonstrated that ultrasound imaging in the diagnosis of fatty liver disease and early atherosclerosis in rats is feasible and efficient, and that carotid IMT increased significantly in NASH rats but not in simple steatotic rats. A significant correlation between the IMT of the carotid artery with hepatic inflammation score were shown in NAFLD rats. This method for non-invasive diagnosis is especially relevant in the research of the pathogenesis and therapy of NAFLD and atherosclerosis using rodent models.