The purpose of this research was to explore the associations of fetuin-A, adiponectin, and fetuin-A/adiponectin ratio (F/A ratio) with subclinical atherosclerosis as evaluated by carotid intima-media thickness (CIMT) in cases with newly diagnosed type 2 diabetes mellitus (T2DM). A total of 283 newly diagnosed T2DM patients were enrolled in this study. Serum fetuin-A and adiponectin levels were determined with an ELISA method. Other clinical and biochemical parameters were also collected. Significant linear increases in waist-to-hip ratio (WHR), systolic blood pressure (SBP), diastolic blood pressure, homoeostasis model assessment of insulin resistance, C-reactive protein (CRP) and F/A ratio, and a significant linear decrease in adiponectin with increasing tertiles of CIMT were observed (P for trends <0.05). However, no significant correlation between fetuin-A and CIMT was detected (P > 0.05). In multivariate logistic regression models, WHR, SBP and F/A ratio were independently correlated with higher CIMT. Receiver operating characteristic curve analysis indicated that F/A ratio had a better predictive power for higher CIMT than adiponectin and fetuin-A, with an area under the curve of 0.802, 0.713 and 0.646, respectively. F/A ratio is an independent indicator of subclinical atherosclerosis in patients with newly diagnosed T2DM.