In conclusion, these data contribute to the concern of the deleterious dyslipidemia found in women with PCOS, with the novel combination of higher levels of ApoE, C3, and HCFII together with lower ApoM being reported here; these dysregulated proteins may circumvent the protective effect of HDL and contribute to a more atherogenic profile that may increase cardiovascular risk and, at least in part, explain the atherogenic, inflammatory, insulin-resistant, and prothrombotic characteristics of PCOS. This evidence concerns the gene APOE and metabolic syndrome.