It is testified that some major genes are actually involved in the malignant transformation of ovarian endometriosis; among these contributing genes, epigenetic inactivation of Runt-related transcription factor 3 (RUNX3) [18], human mutL homolog 1 (hMLH1) [19], E-cadherin (CDH1) [20], Ras-association domain family of gene 2 (RASSF2) [21], and P16 and phosphatase and tensin homolog deleted on chromosome 10 (PTEN) [22] by promoter hypermethylation was well observed; however, long interspersed nuclear element-1 (LINE-1) [23] and syncytin-1 [24] were hypomethylated and activated. This evidence concerns the gene RUNX3 and ovarian endometriosis.