Objective Nonalcoholic fatty liver disease ( NAFLD) is a well-known contributor for the development of cardiovascular disease ( CVD). We examined the influence of NAFLD and metabolic syndrome ( Met S) on markers of subclinical atherosclerosis, including carotid intima-media thickness ( CIMT), brachial-ankle pulse wave velocity (ba PWV) and ankle-brachial pressure index ( ABI), after adjusting for cardiometabolic risk factors. Design A cross-sectional study. Patients and measurements The association between NAFLD, Met S and markers of subclinical atherosclerosis was assessed in 955 participants without CVD using multiple logistic regression analysis after adjusting for multiple cardiometabolic risk variables. Results After adjusting for age and sex, CIMT and ba PWV were found to be significantly correlated with multiple cardiometabolic risk variables, whereas ABI was only associated with obesity parameters. The prevalence of NAFLD differed significantly according to the presence of subclinical atherosclerosis as defined by both CIMT and ba PWV ( P = 0·004 and P = 0·007, respectively). After adjusting for potential confounding factors, NAFLD or Met S was not associated with subclinical atherosclerosis as defined by CIMT and ba PWV. However, individuals with both NAFLD and Met S had a significantly higher risk of subclinical atherosclerosis as defined by CIMT ( OR = 2·06, 95% CI = 1·13-3·74) or ba PWV ( OR = 2·64, 95% CI = 1·46-4·76) compared to normal subjects, even after adjusting for potential confounders. Conclusions The results show that NAFLD and Met S have a synergistic impact on the subclinical atherosclerosis, which suggests that individuals with both NAFLD and Met S should be strongly advised to engage in CVD prevention strategies.