Background: Benign proliferative diseases of the female reproductive system (endometriosis, endometrial hyperplasia, and uterine leiomyoma) are comorbid and often occur together. The aim of the study: To establish common risk factors for the development of benign proliferative diseases of the female reproductive system (endometriosis, endometrial hyperplasia, and uterine leiomyoma). Materials and methods: The review includes up-to-date data from articles found in PubMed and Elibrary on this topic. Results: The article reviews the recent literature about factors determining comorbidity and syntropy of the diseases. Their comorbidity may be based on common environmental risk factors (early menarche, body mass index, induced abortions, etc.) and mechanisms of the pathogenesis, which include hormone-dependent cellular proliferation associated with the action of sex hormones and hormone-independent cellular proliferation processes stimulated by growth factors and cytokines, apoptosis, and pathological neoangiogenesis, etc. These common mechanisms are backed by syntropic genes (e.g., FSHB, COMT). Syntropy and pleiotropy appear to be closely related: syntropic genes manifest pleiotropic effects too. Also, epigenetic factors, such as miRNAs are important determinants of the diseased phenotypes. Conclusion: Identification of the shared factors contributing to the benign proliferative diseases of the female reproductive system helps to determine targets for therapeutic intervention and efficient control of the comorbidity.