Objective: Although, the endometriosis is a benign infllammatory disorder, it mainly causes complications. Thus, trials for better diagnosis and treatment seem necessary. It is supposed that mesenchymal stem cells derived from menstrual blood (MenSCs) in endometriosis patients are different from that of healthy women and so, they are responsible for the crea-tion of the disease. According to the high expression of inflam-matory factors in MenSCs of endometriosis patients, it was sup-posed that the conditioned medium of these cells from healthy women can affect the expression of inflammatory genes. The aim of this study was evaluating the expression of inflammatory genes in endometriosis patients under treatment of conditioned endometrial from MenSCs of healthy women.Materials and Methods: Menstrual blood samples (۱-۲ ml) were collected from endometriosis women and healthy women as control group, in the age range of ۲۲-۳۵ years. Isolation of MenSCs from two groups was performed by the Ficoll-Paque density-gradient method and then endometriosis-derived Men-SCs were treated with conditioned medium from control group in passage three. The expression of inflammatory genes includ-ing IL-۱α, COX-۲, TNF-α, NF-kB and HIF-۱α were assessed using quantitative real-time PCR.Results: Endometriosis-derived MenSCs were morphologi-cally different from healthy MenSCs and also showed higher expression of CD۱۰ marker, which experienced significant de-crease in CD۱۰ marker after ۴ days’ treatment with conditioned medium of healthy MenSCs. Also, after treatment, Endometrio-sis-derived MenSCs showed significant decrease in TNF-α and NF-kB expression but no significant decrease in HIF-۱α.Conclusion: Down-regulation of inflammatory genes in en-dometriosis-derived MenSCs under treatment of conditioned medium derived from healthy MenSCs can be considered as an effective approach for the treatment of endometriosis which needs more investigations.