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Background Carotid artery intima-media thickness (CIMT) and brachial artery flow-mediated dilation percentage (FMD％) are common parameters used for detecting subclinical atherosclerosis.This study compared subclinical atherosclerosis of the carotid and brachial arteries in rheumatoid arthritis (RA) patients and healthy controls using high resolution ultrasonography.We also investigated their correlation with clinical factors and the association between FMD％ and CIMT.Methods One hundred and two RA patients and 46 age-gender matched healthy controls were included in the study.FMD of the brachial artery and CIMT were measured ultrasonographically.Patients with diabetes mellitus,hypertension,renal failure,history of cardiovascular or cerebrovascular disease were excluded.Subjects who were receiving or used high dose steroids were also excluded.Results The CIMT was significantly higher in patients than that in the control group ((0.697±0.053) vs.(0.554±0.051) mm,P ＜0.001),whereas brachial artery FMD％ was lower in patients than that in the controls ((5.454±2.653)％ vs.(8.477±2.851)％,P ＜0.001).CIMT was related to age,disease duration,tender and swollen joint score,C-reactive protein,systolic blood pressure and high-density lipoprotein.However,FMD％ was only association with systolic blood pressure.There was no significant correlation between CIMT and FMD％.Conclusions Compared with the healthy control subjects,RA patients without clinically evident cardiovascular disease had subclinical atherosclerosis in terms of impaired FMD％ and increased CIMT.FMD％ and CIMT may measure a different stage of subclinical atherosclerosis in RA patients.