Background
Accumulated evidence reveals that abnormally expressed genes in eutopic endometrium of endometriosis play a critical role in the pathogenesis of endometriosis.

Aims
Identification of endometriosis‐related genes for further revealing the pathogenesis of endometriosis and offering the basis for developing the molecular‐targeted diagnosis and therapy of endometriosis.

Methods
Forty women with endometriosis and forty control women without endometriosis during their secretory phase were selected for this study. cDNA representational difference analysis (cDNA‐RDA) was performed to screen the up‐regulated genes in eutopic endometrium samples of endometriosis (n = 10) compared with the controls (n = 10). To validate the results, MAT2A, the most abundantly expressed gene, was selected to detect mRNA and protein levels between eutopic endometrium of endometriosis (n = 40) and controls (n = 40) using immunohistochemistry, real‐time fluorescent quantitative PCR and Western blotting.

Results
Ten up‐regulated genes were identified in eutopic endometria of endometriosis compared with controls. Among these genes, COX‐2, BRAF, NRAS and CFL1 have already been reported to be associated with the endometriosis in previous studies. MAT2A, SEPT9, ATAD3A and CADM2 have been reported to be involved in other diseases but not in endometriosis. NAA15 and CCDC21 have not reported in any diseases. Further study showed that MAT2A protein was localised in both endometrial glandular and stromal cells. Compared with controls, the mRNA and protein levels of MAT2A were significantly higher in eutopic endometrium of endometriosis (P < 0.05). Conclusions cDNA‐RDA can be used to effectively identify the endometriosis‐related genes, which can provide novel experimental data and further understand the pathogenesis of endometriosis.