Objective To examine differential messenger RNA (mRNA) expression of relevant cytokines, metalloproteases, growth and adhesion factors in endometrium and peritoneum from women with endometriosis when compared with women without the disease during menstrual and luteal phases of the cycle. Design Patients with endometriosis were compared with control patients. Setting University hospital. Patient(s) A total of 35 patients (20 patients during the luteal phase and 15 patients during the menstrual phase) were selected for this study on the basis of cycle phase and presence or absence of endometriosis. Intervention(s) In this study, endometriosis was laparoscopically and histologically confirmed in 24 women with endometriosis of revised American Society for Reproductive Medicine (ASRM) stage I–II (n = 12) and revised ASRM stage III–IV (n = 12), and the presence of a normal pelvis was documented by laparoscopy in 11 control patients. The macroscopically normal peritoneum tissues were collected from lateral wall left or right, near the colon ascendens or descendens. Main Outcome Measure(s) The expression levels were determined as ratios between the target molecules and β-actin as housekeeping gene. Result(s) In women with endometriosis, peritoneal mRNA levels of matrix metalloproteinase (MMP)–3, transforming growth factor-β, interleukin (IL)-6, and intercellular adhesion molecule-1 and endometrial mRNA levels of MMP-3, tumor necrosis factor (TNF)–α, and IL-8 were significantly higher during the menstrual phase when compared with luteal phase. During the menstrual phase of the cycle, both endometrial expression of TNF-α, IL-8, and MMP-3 mRNA levels and peritoneal expression of transforming growth factor-β, IL-6, and intercellular adhesion molecule-1 mRNA levels were significantly higher in women with endometriosis when compared with controls. Immunohistochemical staining confirmed the presence of TNF-α in peritoneum and endometrium in both women with endometriosis and controls. Conclusion(s) Increased endometrial and peritoneal cytokine mRNA expression during menstruation may contribute to a pelvic inflammatory microenvironment favoring the development of endometriosis.