Endometriosis is an estrogen-dependent, benign gynecological disease, largely defined by the presence of endometrial like tissue in an ectopic location (outside of the uterus). Previous studies have demonstrated increased number of activated B-lymphocytes and excessive production of autoantibodies in endometriosis, which may suggest the importance of follicular T helper (TFH) subsets and follicular T-regulatory (TFR) cells in the pathomechanism of the disease. In the present study, we analysed the distribution of the circulating TFH subsets and TFR cells in endometriosis, and their role in its development. Eleven patients with endometriosis and nine healthy controls were enrolled in our study. Peripheral blood lymphocyte subgroups were quantified by flow cytometry. We found no difference in the percentages of activated circulating TFH cells and TFR cells in endometriosis patients compared to controls. Among the circulating TFH subsets, we observed the same cellular distribution in endometriosis as in healthy individuals. Although over-activation of B-cells as well as autoantibody production could be potentially linked to an altered TFH cell activation and function; our results suggest that in the pathogenesis of endometriosis, an enhanced TFH-B cell interaction may not play an important role.