The incidence of endometriosis is nearly 15% among women of childbearing age with the pathogenesis been a research focus. The classic theory may encounter plentiful challenges, because it can′t account for the occurrence of ectopic lesions located in special areas distant from pelvic, while stem cell theory tries to demonstrate the pathogenesis of various kinds of ectopic lesions with "monism" point of view. Adult stem cells involved in endometriosis lesions may originate from the endometrium, bone marrow, ovary and other sources. Various kinds of molecules, such as estrogen, chemokines, epidermal growth factor, platelet -derived growth factor and other factors involved in differentiation of adult stem cell. The change of microRNA levels and epigenetic may be related to regulate the differentiation of mesenchyme stem cells into endometrial-like cells. Abnormal colonization of stem cells may change the uterine receptivity, leading to infertility, miscarriage and other adverse reproductive outcomes. Among different types of endometriosis formed, the gene expression of stem cells of peritoneal and deep infiltrating was similar, which is different from that of eutopic endometrial stem cells. With the deepening of research, stem cells are commonly used in the field of obstetrics and gynecology and have promising prospects in the treatment of premature ovarian failure, Asherman syndrome, endometriosis related infertility and targeted drug development [ABSTRACT FROM AUTHOR]