BACKGROUND: Atherosclerosis as a cardiovascular disease was found to begin even in the fetal period. However, information about risk factors of pre-clinical atherosclerosis in childhood has been limited. Hence, this study was aimed to find out the risk factors of atherosclerosis by measuring the carotid artery intima-media thickness in children. High resolution B-mode ultrasound used to examine the carotid artery intima-media thickness was demonstrated to be useful in finding the early carotid structural changes. METHODS: The study included 79 children who were divided into two groups according to their ages: group I consisted of 42 children with ages from 5 to 9 years and group II consisted of 37 children with ages from 10 to 18 years, Among them, 23 had a positive family history for risk, such as hypertension, obesity or dyslipidemia. Blood samples were collected and total cholesterol, triglycerides, high density lipoprotein and low density lipoprotein were assayed. The carotid artery intima-media thickness was measured by ultrasound. Comparisons were done between the two groups using Student’s t tests and Chi-square analysis. Body mass index, blood pressure, levels of lipids, family history and the carotid artery intima-media thickness were calculated by conditional logistic regression analysis. RESULTS: Compared with the children without a positive family history, the incidence of the increased carotid artery intima-media thickness was significantly high (chi(2) = 4.364, P < 0.05). There were no statistically significant differences between left and right carotid arteries in carotid artery intima-media thickness (P > 0.05). In this study, diastolic blood pressure and the atherosclerosis index were suggested to be the risk factors to the thickened carotid artery intima-media thickness. In group I the diastolic blood pressure’s odds radio was 1.187 (P = 0.035) and the atherosclerosis index odds radio was 37.165 (P = 0.001); in group II the diastolic blood pressure’s odds radio was 1.371 (P = 0.009) and the atherosclerosis index odds radio was 30.724 (P = 0.015). CONCLUSION: The diastolic blood pressure and atherosclerosis index were the risk factors in pre-clinical arthrosclerosis. Regularly monitoring the high-risk children for the development and progression of vascular lesion would be of great value in avoiding and preventing cardiovascular disease.