Background: The purpose of this study was to investigate the association between lipoprotein(a) [Lp(a)] concen-trations, apolipoprotein(a) [apo(a)] isoform, and coronary artery disease (CAD) stratification in Han Chinese.Methods: Logistic regression analysis was performed to analyze the association between Lp(a) concentrations, apo(a) isoform and CAD stratification. Lp(a) concentrations and apo(a) isoforms were combined with other risk factors to establish the optimal prediction model of CAD risk.Results: Individuals with the top quarter of Lp(a) concentrations had more than a two-fold higher risk of stable CAD and three-fold higher risk of acute coronary syndrome (ACS) compared with those in the bottom quarter. This association was no longer significant after adjustment for apo(a) isoforms in stable CAD (OR 2.198, 95% CI 0.991 -4.875, p = 0.053), but remained significant in the ACS (OR 3.583, 95% CI 1.278 -5.614, p < 0.05). Individu-als with small apo(a) isoforms had more than a two-fold higher risk of stable CAD and almost three-fold higher risk of ACS compared with those carrying larger apo(a) isoforms; however, this association was significantly alle-viated after adjustment for Lp(a) concentrations (OR 2.133, 95% CI 0.964 -4.742, p = 0.098; OR 2.642, 95% CI 1.032 -5.833, p = 0.298, respectively). A combination of Lp(a) concentrations and apo(a) isoforms with other risk factors was the optimal prediction model of CAD risk (AUC 0.800, 95% CI 0.752 -0.848, p < 0.001).Conclusions: Elevated Lp(a) concentrations and small apo(a) isoforms were significant risk factors for CAD strat-ification, and their effects on CAD risk were mediated by each other. Combined application of Lp(a) concentra-tions and apo(a) isoform with conventional risk factors could aid in the assessment and prediction of CAD.