Müllerian anomalies are congenital conditions characterized by the incomplete development of the female reproductive tract. Women affected by Müllerian anomalies often display additional malformations of the renal, skeletal, and cardiovascular system, and are at a higher risk for infertility and adverse pregnancy outcomes. Several Müllerian anomalies have been reported in association with endometriosis, but it is unclear if all classes or anatomical variations are associated with the disease. Most importantly, both Müllerian anomalies and endometriosis can manifest with a wide degree of variability, adding further complexity to their poorly defined relationship. Retrograde menstruation occurring in obstructive Müllerian anomalies is a well-accepted mechanism for the development of endometriosis. However, endometriosis can occur following surgical correction of the anomaly or in the absence of obstruction. This suggests that other mechanisms may be involved, although the specific pathogenesis remains elusive. This review provides a comprehensive summary of the current state of clinical research on endometriosis in Müllerian anomalies. This review also highlights research and knowledge gaps, informing the development of future experimental designs to address current limitations including heterogeneity of phenotypes, variable comorbidities, and lack of genetic information.