Endometriosis is the growth of endometrial tissue outside the uterine cavity. It affects 6–15% of young women, causing pain and Infertility. Surgery is required for diagnosis and treatment, but recurrence is frequent (33–75% in <5 years). Its etiology is unknown. We hypothesised that endometrial stem/progenitor cells are shed during menstruation and gain access to the peritoneal cavity by retrograde flow where they initiate endometriosis lesions in susceptible women. We recently discovered rare cells with epithelial progenitor cell and mesenchymal stem/stromal cell (MSC) activity in human endometrium1, which may be responsible for its remarkable regenerative capacity. We have identified 2 candidate markers of human endometrial epithelial progenitor cells, H3D12 and Adm2, which are predominantly located in gland profiles in the basalis layer. Markers identifying endometrial MSC, (eg W5C52) show that these cells are found in the functionalis and basalis in a perivascular location. Cells isolated from samples of uterine menstrual blood, peripheral blood and peritoneal fluid collected from menstruating women undergoing laparoscopy were assessed for clonogenicity, and expression of H3D12, Adm2 and W5C5. In menstrual blood, there was no difference in the concentration of clonogenic, H3D12+, Adm2+ and W5C5+ cells between endometriosis or control samples. No H3D12+, Adm2+ or W5C5+ cells were found in peripheral blood from either group. While the volume of peritoneal fluid was similar from women with and without endometriosis, the concentration of viable cells, Adm2+ and W5C5+ cells was significantly elevated in the endometriosis group. Our data suggest that in women with endometriosis, there may be preferential shedding of endometrial stem/progenitor cells into the pelvic cavity during menstruation compared to controls, where their greater ability to survive may enable them to initiate endometriosis lesions.