HOXA10 is an important gene for endometrial receptivity and plays a regulatory role in the adult female reproductive tract. It is regulated by epigenetic modulation in the CpG clusters of promoter in some cases. The aim of this study was to investigate HOXA10 expression and the epigenetic regulation in the eutopic endometrium of fertile women with endometriosis by quantitative real-time polymerase chain reaction (RT-PCR) and Western blot. The effect of 5-azacytidine (5-ac), a demethylation agent on HOXA10 expression was determined on endometrium stromal cells (ESCs) from these women with endometriosis. Results revealed that in normal endometrium (NE), HOXA10 messenger RNA (mRNA) and protein expression at the secretory phase were significantly higher than that at the proliferative phase. The HOXA10 mRNA and protein expression in the eutopic endometrium of endometriosis were significantly lower than in NE. The HOXA10 mRNA and protein levels in cultured stromal cells from endometriosis in vitro were significantly increased in a 5-ac treatment group compared with a nontreatment group. Our results indicated that the level of HOXA10 decrease in the eutopic endometrium of patients with endometriosis. Upregulation of HOXA10 in ESCs after treatment with 5-ac suggests that HOXA10 expression is controlled by methylation of the promoter. An epigenetic aberration is likely the main cause of endometriosis.