Background: Bilirubin has been recognized as a potential endogenous inhibitor of atherosclerosis, being inversely associated with carotid intima-media thickness (CIMT). However, little information is available concerning the correlation between serum indirect bilirubin (IBIL), especially long-term IBIL level, and early atherosclerosis progression. This study was designed to evaluate the relationship between serum IBIL level and CIMT progression. Methods: A total of 2205 participants were enrolled in this Asymptomatic Polyvascular Abnormalities Community study (APAC study). CIMT was measured at baseline and 2-year follow-up. The participants were divided into four groups based on their serum IBIL levels at baseline. Both baseline and average serum IBIL values during the 2-year follow up were used in the analysis. Multivariable logistic regression and linear regression were used to assess the associations between serum IBIL and CIMT progression. Results: The results showed that 51.93% (1145/2205) of participants were diagnosed with CIMT progression during the 2-year follow-up. Baseline serum IBIL level was significantly associated with the incidence of CIMT progression after adjusting for other potential confounding factors. Compared with the first quartile, adjusted odds ratios (OR) of the second, third, and fourth quartiles of IBIL were 0.70 [95% confidence interval (CI), 0.55-0.90], 0.68 (95% CI. 0.52-0.87), and 0.63 (95% CI, 0.49-0.82) (P - 0.0006), respectively. Serum IBIL level during the follow-up was also associated with CIMT progression in the univariate analysis (P = 0.0022), although no longer significant after adjusting for potential confounders in the multiple linear regression. Conclusion: The study demonstrated the inverse relationship between serum IBIL and CIMT progression. Lower serum IBIL level is an independent predictor of subclinical atherosclerosis.