Pelvic pain, infertility and a high postoperative recurrence rate are associated with endometriosis and adversely affect the physical and mental health of patients. Moreover, these factors place a heavy burden on families and society. The identification of endometrial stem cells (EnSCs) in the eutopic endometrium, menstrual blood and ectopic lesions of women with endometriosis not only provides new research objects in the context of endometriosis but also promotes and improves our understanding of its pathogenesis. Furthermore, based on previous studies, we reasonably suppose that dysfunctions of eutopic EnSCs play a critical role in the onset of endometriosis and directly cause abnormalities in the endometrium; subsequently, retrograde menstruation facilitates the delivery of abnormal endometrial tissues to the ovaries and pelvic cavity, where they ectopically implant, grow and form ectopic lesions. Additionally, as a chronically progressive disease, there is a delay (3-11 years) from the first onset of symptoms to the diagnosis of endometriosis. Therefore, the development of a method for early diagnosis with high sensitivity and specificity is essential for endometriosis patients and has the potential to enable early treatment, prevent endometriosis progression and relieve pain in patients. Thus, focusing on EnSCs will contribute to clarifying the potential pathogenesis of endometriosis and provide support for the application of EnSCs as therapeutic and early diagnostic targets in endometriosis treatment.© The Author(s) 2020. Published by Oxford University Press on behalf of Society for the Study of Reproduction.