Objective: To compare the distribution of ApoE polymorphisms between women with PCOS and healthy controls to explore whether specific ApoE genotypes contribute to the genetic susceptibility of developing PCOS, and to investigate the association between APOE gene polymorphisms and lipid profiles in PCOS patients. Methods: A case-control study was conducted between November 2023 and January 2025, enrolling 120 women with PCOS diagnosed according to Rotterdam criteria and 60 age-matched healthy controls. Participants underwent comprehensive clinical assessment, hormonal evaluation (FSH, LH, total and free testosterone), lipid profiling, and inflammatory marker analysis. DNA extraction was performed from whole blood, followed by PCR amplification and direct sequencing of ApoE gene fragments containing SNPs rs429358 and rs7412. Results: PCOS participants demonstrated significantly higher age, body weight, and height compared to controls (p<0.05). Hormonal analysis revealed characteristic PCOS patterns with elevated LH, total testosterone, free testosterone, and C-reactive protein levels, alongside reduced FSH concentrations (p<0.001). Lipid profile analysis showed significantly higher total cholesterol and LDL levels, with lower HDL concentrations in PCOS patients (p<0.05). Genetic analysis identified three ApoE genotypes (ε3ε3, ε2ε3, ε3ε4), with ε3ε3 being most prevalent in both groups. No significant differences were observed in ApoE genotype or allele distribution between PCOS patients and controls (p>0.05). However, within the PCOS group, ε4 allele carriers exhibited significantly elevated total cholesterol (p=0.039), triglycerides (p=0.013), and VLDL levels (p=0.026) compared to ε2 and ε3 carriers. Conclusions: ApoE gene polymorphisms do not appear to significantly influence PCOS susceptibility, as genotype distributions were comparable between patients and controls. However, ApoE variants, particularly the ε4 allele, may modulate metabolic dysfunction severity in women with established PCOS, potentially affecting cardiovascular risk stratification and therapeutic management approaches.