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Syntax score (SS) and Gensini score (GS) are used to determine the complexity and severity of coronary artery disease. Although there are some studies indicating the individual relationship of these scoring systems with the carotid intima–media thickness (cIMT) and epicardial fat tissue (EFT), there was no previous study that compared the SS and GS in that respect. We aimed to assess the relationship of SS and GS with predictors of atherosclerosis. We enrolled 522 patients. There were positive correlations between GS and SS tertiles with cIMT and EFT. According to multivariate linear regression analysis for GS, EFT (β: 0.035, t: 2.63, and P = .49) and cIMT (β: 0.339, t: 2.97, and P = .053) were not independently associated. For SS, EFT (β: 0.009, t: 6.5, and P = .006) and cIMT (β: 1.2, t: 10.1, and P = .001) were independently and significantly associated. We showed that the SS is significantly associated more with surrogate markers of atherosclerosis such as EFT and cIMT than the GS.