In the present study, we investigated the relationship between the rs4420638A/G and -317H1/H2 polymorphisms of the apoC1 gene and the risk of PCOS, evaluated the effects of the genotypes on clinical and metabolic indexes and PAF-AH activity and defined the association of apoC1 gene variations with apoE allele status in southwest Chinese women with or without PCOS using relatively large sample sizes. This evidence concerns the gene APOE and polycystic ovary syndrome.