Bilirubin may have important antiatherosclerotic effects. Prediabetes (PD), the intermediate stage before diabetes mellitus, is associated with increased cardiovascular morbidity and mortality. We evaluated the relationship between serum bilirubin levels and carotid intima-media thickness (cIMT), as a surrogate marker of subclinical atherosclerosis, in patients with PD. We enrolled 170 consecutive patients with PD. The patients underwent ultrasonography to evaluate cIMT. The patients were divided into groups according to cIMT values (<0.9 vs ≥0.9 mm). The patients with cIMT ≥ 0.9 mm had significantly higher diastolic blood pressure, neutrophil-lymphocyte ratio (NLR), and glycated hemoglobin values compared with patients having cIMT < 0.9 mm, whereas total and direct bilirubin values were significantly lower in this group. Multivariate regression analyses revealed NLR and total bilirubin as the independent predictors of subclinical atherosclerosis. The present study demonstrated that NLR and lower total bilirubin levels were independent predictors of subclinical atherosclerosis in patients with PD. Simple measures such as NRL and total bilirubin may provide predictive information regarding the risk of cardiovascular disease in patients with PD.