Background: To investigate the association between apolipoprotein E (APOE) gene polymorphisms and coronary heart disease (CHD) risk within a localized Mongolian clinical cohort.

Methods: This hospital-based case–control study recruited 63 patients with angiographically confirmed CHD and 61 sex-matched healthy controls. Anthropometric measurements and lipid profiles and pathways for APOE genotypes were strictly assessed. This exploratory hospital-based case–control study was not designed as a nationally representative population-based survey, and participant recruitment was limited to a single tertiary referral center in Mongolia.

Results: High-density lipoprotein cholesterol levels were significantly higher in the case group than in the control group (1.56 ± 0.14 vs. 1.33 ± 0.18 mmol/L, P < .001), while total cholesterol was significantly lower in cases than in controls (3.91 ± 0.60 vs. 5.34 ± 0.80 mmol/L, P < .001). The distribution of APOE genotypes (ε2/ε3, ε3/ε3, ε3/ε4, and ε4/ε4) differed significantly between the case and control groups (P = .009). Both systolic and diastolic blood pressure significantly correlated with waist circumference (P = .026). Multivariable logistic regression revealed that the ε2/ε3 genotype was associated with significantly lower odds of disease (odds ratio [OR] = 0.29, P = .007, 95% CI: 0.12-0.71), whereas ε4-related findings were highly imprecise due to sparse genotype counts and lacked statistical significance (OR = 1.07, P = .930, 95% CI: 0.23-5.02).

Conclusion: This study showed a significant association between the APOE genotype and CHD in a Mongolian population. These findings highlight the importance of considering qualitative aspects of lipid metabolism, rather than total cholesterol alone, and suggest that genetic factors, including APOE polymorphisms, may contribute to CHD risk independently of absolute cholesterol levels, underscoring the need for population-specific cardiovascular risk assessment.