OBJECTIVES: This systematic review aimed to investigate the association between genetic polymorphisms in estrogen receptor alpha (ERα) and beta (ERβ) and the presence and severity of temporomandibular disorders (TMDs). MATERIALS AND METHODS: A comprehensive search was conducted in PubMed, Scopus and Web of Science on October 19, 2024, without language or time restrictions. Studies were included if they were cross-sectional, case-control, or cohort designs and reported data on ER-polymorphisms and TMDs, diagnosed using validated criteria. Two independent reviewers screened the results to identify eligible studies. Data were extracted and synthesized narratively due to high heterogeneity across included studies, with a subgroup analysis performed to evaluate the influence of sex. The risk of bias was assessed using the Joanna Briggs Institute's critical appraisal tools. RESULTS: The search identified 277 articles, of which 8 studies met the inclusion criteria. Seven were case-control and two cross-sectional studies. The most commonly investigated ER polymorphisms were ESR1 (Pvu II and Xba I) and ESR2 (rs1676303). Some studies identified associations between specific polymorphisms and TMD-related pain or joint conditions, although results varied across different populations and subtypes of TMDs. CONCLUSIONS: The findings suggest potential associations between specific ERα and ERβ polymorphisms and TMD risk, particularly in women. However, inconsistencies across studies underscore the need for prospective and larger studies to confirm these genetic links and clarify their clinical significance. SYSTEMATIC REVIEW REGISTRATION: CRD42024581266.