This study was performed to investigate the expression of cathepsin B mRNA and protein in eutopic and ectopic endometrial tissues of patients with endometriosis and in normal endometrial tissues and to clarify the association between the cathepsin B expression and endometriosis. A total of 40 women with histologically confirmed endometriosis were recruited for study group. For controls, 20 women undergoing operative treatment for uterine myoma, cervical intraepithelial neoplasia (CIN) or benign gynecologic conditions other than endometriosis were recruited. Eutopic endometrial tissues of both groups and ectopic endometrial tissue of study group were collected during the operations. We employed real time reverse transcriptase - polymerase chain reaction (RT-PCR) to quantify mRNA levels of cathepsin B in these tissues. Then, we performed western blot analysis to measure the protein levels of cathepsin B. The expressions of cathepsin B mRNA and protein were significantly higher in both eutopic and ectopic endometrial tissues of women with endometriosis than in endometrial tissues of controls. These data suggest that the higher expression of cathepsin B in the endometrial tissues might be associated with the development of endometriosis. In addition, eutopic endometrium itself with higher expression cathepsin B may play a pivotal role in the histogenesis of endometriosis.