Purpose Müllerian duct anomalies (MDAs) are congenital malformations of the female reproductive tract with complex genetic determinants. We evaluated the association between gene polymorphic variants and MDA susceptibility.Methods PubMed, Embase, and Scopus were searched to September 2025 (PROSPERO: CRD420251143377). Risk of bias, evidence certainty, and association credibility were assessed using the Newcastle-Ottawa Scale, GRADE, and Venice criteria, respectively. Pooled odds ratios (ORs) were estimated under six genetic models with false discovery rate correction.Results Twelve studies (2,179 cases; 2,207 controls) were included. WNT9B rs4968281 showed nominal associations under recessive (OR = 0.64, 95% CI: 0.43–0.96) and codominant (OR = 0.69, 95% CI: 0.53–0.89) models, but neither remained significant after correction. Evidence certainty was very low, and two studies showed Hardy-Weinberg disequilibrium. TBX6, PAX2, and PBX1 variants were identified as candidates for further investigation.Conclusions Larger, ethnically diverse, well-characterized cohorts are needed to clarify these findings.
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