Background: Approximately 15% of all rare diseases occur with orofacial manifestations. Symptoms and manifestations of relevance to orthodontists represent a considerable proportion of these diseases and require appropriate strategies for their treatment. This article provides an overview of the orthodontically relevant manifestations of rare diseases. Material and Methods: Overall, 3,639 rare diseases listed at the Orphanet, OMIM or Pubmed database were evaluated for orofacial manifestations. All rare diseases which were indicated with at least one orofacial manifestation were recorded in a database for rare diseases with orofacial manifestations called “ROMSE,” which was developed by the authors. All the rare diseases were analysed with regard to orthodontically relevant orofacial manifestations, such as dysgnathia, changes in the number of teeth, failures of eruption, pathologies of bone metabolism or orofacial clefts. For all rare diseases with orthodontic relevance, an exact analysis was undertaken. Results: The orthodontically relevant orofacial manifestation termed dysgnathia is described in 151 of 535 identified rare diseases (28.2%). In these 151 rare diseases, 15 different subforms of dysgnathia, in the sense of skeletal misdevelopments of the jaws but without dental abnormalities, were described. Also changes in the number of teeth (17.9%), orofacial clefts (27.6%), failures of eruption (8.4%) and pathologies of the bone (2.1%) were described. Conclusions: Orthodontics play an important role in the diagnosis and treatment of orofacial manifestations in rare diseases. Databases such as ROMSE are a first step toward providing valid information in publicly accessible databases.