OBJECTIVE Recurrent aphtous stomatitis (RAS) is an inflammatory oral mucosal disease. It has been known that inflammatory cascade plays important role in the atherosclerotic process. The aim of the study was to investigate the relationship between subclinical atherosclerotic findings and a systemic inflammatory disease, RAS. METHODS In total, 32 patients with RAS were matched with 30 control subjects on the basis of age, sex, and major cardiovascular risk factors. Laboratory parameters including lipid profiles were determined for patients and controls. B-mode ultrasonography was used to assess carotid extra-medial thickness (cEMT) and carotid intima-media thickness (cIMT). RESULTS Both cEMT and cIMT in the RAS group were significantly higher than in the control group (P = 0.002 and 0.013, respectively). There was a significant positive correlation between cIMT and cEMT (r = 0.381, P = 0.034). cIMT was positively correlated with age, triglyceride levels, and systolic blood pressure, while cEMT was positively correlated with age in patients with RAS. CONCLUSIONS To our knowledge, this is the first reported study to evaluate cEMT and cIMT in patients with RAS. This study presents morphological evidence of subclinical atherosclerosis in patients with RAS. Further studies investigating the relationship between atherosclerosis and RAS are needed.