Endometriosis is a complex clinical syndrome that impairs many aspects of a woman's life, characterized by a chronic estrogen-dependent inflammatory process, mainly affecting the pelvic organs, with ectopic presence of tissue analogous to the uterine mucosa (endometrium). Despite intensive research in the field of etiopathogenesis, its cause has not yet been determined, and treatment remains symptomatic. Endometriosis causes two main complications, i.e. pelvic pain syndrome and infertility. In recent years, thanks to the analysis of the human microbiome, it has become possible to deepen the knowledge of the physiological and pathological interactions between microorganisms inhabiting various body areas and the host. Bacteria may enter the peritoneal cavity in the mechanism of retrograde menstruation and translocate from the intestines, and then promote the development of local and systemic inflammation, leading to the symptoms of endometriosis. The study is to determine whether the presence of a specific intestinal, peritoneal and uterine microbiome correlates with endometriosis stage and whether its presence predisposes to increased pain or infertility. Concordance or divergence of bacterial populations inhabiting the peritoneal and uterine cavities could have clinical implications, i.e. the possibility of empirical antibiotic therapy in patients undergoing only endometrial aspiration biopsy and not opting for surgical treatment.