Endometriosis is a common multifactorial disease caused by an interaction between multiple gene loci and environment. Four genome-wide association studies (GWASs) of endometriosis have identified several single-nucleotide polymorphisms (SNPs) associated with endometriosis. However, results from independent replication studies with different populations are inconsistent. The present study aims to evaluate whether the GWAS-derived susceptibility loci are correlated with the risk of the development of ovarian endometriosis in North Chinese women. This case-control study comprised 580 patients with ovarian endometriosis and 606 matched control women. Three SNPs were selected for this association study including rs10965235 in CDKN2BAS, rs2235529 located in LINC00339-WNT4, and rs12700667 in an intergenic region on 7p15.2. The results show that the G/A genotype of rs12700667 can significantly increase the risk of developing ovarian endometriosis when compared with the G/G genotype (odds ratio [OR] = 1.57, 95% confidence interval [CI] = 1.23-2.00). Similarly, the carriers with A allele showed a higher risk of ovarian endometriosis than those with G allele (OR = 1.23, 95% CI = 1.12-1.68). The study suggests that the endometriosis-associated genetic polymorphisms (rs12700667) from GWAS be associated with the risk of developing ovarian endometriosis in North Chinese women.