Fifteen percent of the 5000 to 8000 rare diseases (RDs) can manifest in the oral and maxillofacial region. Little attention has been paid to the care situation of people with RDs in dentistry. Hence, the aim of this study was to assess the level of knowledge about RDs among dentists at a university hospital (DUs) compared to dentists with different professional backgrounds and among general dentists, specialist dentists and DUs in the chamber district of Westfalen-Lippe. Moreover, self-assessment of the level of knowledge was evaluated. A questionnaire was designed, which was made available digitally via a link. A random sample of 1500 dentists, specialist dentists, and oral- and craniomaxillofacial surgeons from the membership of the Dental Association of Westfalen-Lippe, and all dentists, specialist dentists, and oral- and craniomaxillofacial surgeons working at the University Dental Hospitals Münster and Witten/Herdecke, were invited to participate to our study. Differences in the level of knowledge between DUs and non-DUs and differences between DUs, general dentists, and specialist dentists were tested via two-sided Fischer’s exact tests. Differences between the three groups of self-assessment of the level of knowledge and the self-assessment of how sufficient their own knowledge about RDs is were tested via two-sided Kruskal–Wallis tests. The global level of significance was controlled by the Bonferroni method. A total of 267 questionnaires were completed, of which 64.0% were answered by general dentists, 25.5% by specialist dentists and 10.5% by DUs. DUs had a significant higher level of knowledge about RDs (adjusted p = 0.012) compared to non-DUs and achieved higher scores (median = 16.5 points) than general (median = 13 points) and specialist dentists (median = 13 points) (p = 0.001). In the self-assessments, the differences were not significant (p > 0.05). In conclusion, most participants showed no or little knowledge about RDs, and DUs had a significant higher level of knowledge than non-university dentists.