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Endometriosis is a common, benign gynecological disease which is determined as an overspreading of endometrial tissue in exterior region of the uterine cavity. Evidence suggests that retrograde menstrual blood which contains mesenchymal stem cells with differential gene expression compared to healthy women may play a role in endometriosis creation. We aimed to identify whether the conditioned medium (CM) from menstrual blood-derived mesenchymal stem cells (MenSCs) of healthy women can affect the expression level of inflammatory and stemness genes of MenSCs from endometriosis women. Endometriosis-derived MenSCs (E-MenSCs) were treated with CM derived from healthy women's MenSCs (non-endometriosis derived MenSCs [NE-MenSCs]). Some CD markers were analyzed by flow cytometer before and after treatment compared with NE-MenSCs, and the expression level of inflammatory and stemness genes was evaluated by real-time PCR. E-MenSCs show different morphology in vitro culture in comparison with NE-MenSCs, which were changed in the presence of CM, into a morphology more similar to normal cells and showed significant decrease expression of CD10 after CM treatment. In our results, the interleukin-1, cyclooxygenase-2, and hypoxia-inducible factor 1α as inflamaturay genes and octamer-binding transcription factor 4, NANOG, and sex determining region Y-box 2 as stemness genes showed significantly different expression level in E-MenSCs after treating with CM. Our study indicates that the expression level of some inflammatory- and stemness-related genes which have differential expression in E-MenSCs compared with NEMenSCs, could be changed to normal status by using CM derived from NE-MenSCs.