Background: Rare diseases (RDs) are serious often chronic progressive diseases that affect a smaller number of individuals. RDs can manifest in any region of the body and have systemic effects that are detrimental to individual health. Although RDs are individually rare, there are various debilitating disorders arising from RDs. One of the disorders that have been shown to have a negative impact on the health of RD patients is temporomandibular disorders (TMD). There is a dearth of data on the rare diseases and potential manifestations of TMD. The objective of this systematic review is to provide an overview of rare diseases and temporomandibular joint (TMJ) manifestations.Method: The criterion for analysis of a rare disease and temporomandibular manifestations was inclusion in the Orphanet Classification of Rare Diseases and/or the National Organization for Rare Disorders (NORD)/The Genetic and Rare Diseases (GARD) databases. Only rare diseases with TMJ manifestations were recorded.Results: A total of 54 RDs with TMJ manifestations and different TMD diagnoses were recorded. There were thirty-five studies derived from the Pubmed search, and the Orphanet input had 19 results. Overall, 13 different types of TMJ manifestations and TMD diagnoses were recorded in rare diseases.Conclusion: TMJ manifestations associated with rare diseases are not uncommon. Healthcare professionals can play an important role in diagnosing and managing the complexity of RDs with TMJ manifestations. A multidisciplinary approach to TMD patients with rare diseases is advisable.