The degree of linkage disequilibrium (LD) among the apoE ε2/ε3/ε4, and the apoC1 rs4420638A/G and -317H1/H2 genetic polymorphisms was analyzed in patients with PCOS and the controls, with all found to be in moderate to reasonably high LD with each other: apoC1–317H1/H2 loci and apoE ε2/ε3/ε4 loci (D’ = 0.970, r2 = 0.702), apoC1–317H1/H2 loci and rs4420638A/G loci (D’ = 0.910, r2 = 0.455), and apoC1 rs4420638A/G loci and apoE ε2/ε3/ε4 loci (D’ = 0.758, r2 = 0.397). The gene discussed is APOE; the disease is polycystic ovary syndrome.