Uterine endometrium contains numerous bone marrow-derived cells. The spectrum of cell types is different from that of any other tissue, and the differences in endometrium from women with endometriosis may reflect a different endometrial phenotype in these women. The cell types of bone marrow origin found in ectopic endometrium may indicate the degree of differentiation of the tissue. It was found that, in normal endometrium, the CD45+ cell population comprised T cells, macrophages, CD56+ large granular lymphocytes, some CD16+ cells and a few B cells. Changes in these cell populations during the menstrual cycle were similar in endometrium from both controls and patients with endometriosis, and resembled that reported previously by others. In ectopic endometrium, the frequency of CD45+ cells remained within the same range as that of uterine endometrium but without any obvious pattern of change during the menstrual cycle. CD56+ large granular lymphocytes, an immune cell type characteristic of uterine endometrium, were also found in ectopic endometrium. Our results indicate that ectopic endometrium, as well as comprising both glandular and stromal cells, contains bone marrow-derived cell populations similar to those of uterine endometrium. This suggests that the same processes of cell migration and/or differentiation occur in ectopic and uterine endometrium.