Recent studies indicated that there is a high density of small nerve fibers in the functional layer of the endometrium in women with endometriosis and that it can be used as a marker to detect endometriosis. In this study, the efficacy assessment of small nerve fibers' density as a diagnostic marker was compared in patients with and without endometriosis. In this study, women with history of pelvic pain and/or infertility who were candidates for laparoscopy or laparotomy in Rassoul hospital (2007-2009) were enrolled. Histological sections of endometrial tissue were prepared from endometrial biopsy from women with endometriosis (n = 12) (1) and without endometriosis (n = 15) (2). Protein gene product 9.5 and neurofilament were evaluated as marker from endometrial biopsies by immunohistochemical methods. There was no statistically significant difference between two groups according to age, body mass index. Nerve fibers were detected in all endometrial biopsies from all women with endometriosis but detected only in three women without endometriosis. The mean density of nerve fibers was 2.2 ± 4.7 mm(-2) in group without endometriosis and) 13.1 ± 3.3 (in group with endometriosis (p < 0.001). Women with endometriosis had significantly higher nerve fiber density in comparison with women without endometriosis. Our findings indicated that endometrial biopsy for detecting density of nerve fibers by usage of protein gene product 9.5, provided a reliable marker for diagnosis of endometriosis