Endometriosis is a chronic multifactorial disease that affects one in ten women of reproductive age. Genetic, endocrine and immunological factors play an important role in the pathogenesis of endometriosis. In recent years, an increasing number of studies have been devoted to the role of vaginal microbiota in the pathogenesis of endometriosis. However, the role of viral infections, such as papillomavirus and herpesvirus infections, in the development of the disease has not been sufficiently studied. The review highlights current ideas about the role of human papillomavirus and herpesvirus infections in the genesis of endometriosis. The data obtained have convinced us of the need to further search for new relationships between papillomavirus and herpesvirus infections, microbiota of reproductive organs and pathogenesis of such a complicated disease as endometriosis.