Immunological changes and gene expression anomalies are involved in the etiopathophysiology of endometriosis, although how these alterations are connected is not well established. The aim of this study was to determine the relationship between levels of immune cell populations, cytokines and CA-125 in peritoneal fluid (PF) and 'chocolate' cyst fluid (CF), and aromatase expression in endometriotic tissue, as well as to investigate any association with symptoms or recurrence of the disease. Eutopic and ectopic endometrium, CF and PF were collected from 84 women with endometriomas and 24 with benign non-functioning ovarian tumors undergoing radical or conservative surgery. Immunohistochemistry was performed to determine aromatase expression. PF cell populations were assessed by flow cytometry, and CF and PF levels of interleukin (IL)-6, IL-8, IL-13, IL-17 and CA-125 were quantified by ELISA. These parameters were compared with aromatase expression, symptoms and recurrence of the disease. IL-6 levels in PF were higher in patients with endometriosis than in patients with benign non-functioning ovarian cysts, and correlated positively to dysmenorrhea and pelvic pain in the first group. An association between PF IL-8 and CA-125 was also observed in endometriosis. Aromatase positive patients showed higher levels of PF CA-125 and CF IL-17. Recurrence of symptoms or endometrioma occurred sooner in patients having higher IL-6 or IL-8 levels in CF, respectively. These findings suggest an association of IL-6 with pain in endometriosis, as well as a relationship between cytokine expression and recurrence of the disease. However no clear relationship between aromatase expression and other parameters was found.