Expression of estrogen receptor exon 5 splicing variant (ER-E5SV) mRNA contributes to dominant positive properties and metastatic potential of gynecological cancers. Therefore, in endometriotic endometria, which conserve implantation and tumor-like spreading potentials, the expression of ER-E5SV and estrogen receptor wild type (ER-WT) mRNA was analyzed, to investigate the biological implications. Estrogen receptor wild type mRNA in normal endometria was downregulated after ovulation, but not in endometriotic endometria. Therefore the wild type cascade in endometriotic endometria might be partly disorganized. The level of ER-E5SV mRNA in endometriotic endometria was lower than that in normal endometria, regardless of the stage in the menstrual cycle. However, there was no significant difference in the ratio of ER-E5SV to ER-WT mRNA in both normal and endometriotic endometria. On the other hand, the level of ER-E5SV mRNA in both normal and endometriotic endometria did not vary during the menstrual cycle. The dominant positive behavior of ER-E5SV might be masked by the functional cascade of ER-WT in normal endometria, but not in endometriotic endometria. This status might result in an incomplete response to endogenous steroids, and contribute to implantation and spreading potentials of endometriosis.