Background: The aim of this study was to collect information on oral health-related quality of life (OHRQoL) in people with rare diseases. Methods: A questionnaire comprising free text questions and the German version of the standardized Oral Health Impact Profile-14 (OHIP-14) questionnaire on OHRQoL was developed. All participants who indicated oral symptoms in the questionnaire were included in a cluster analysis. Different cluster analyses were performed (Ward’s, k-Means) to find symptom profile groups in the data. Results: A total of 484 questionnaires with 96 rare diseases were included in the study. The most reported symptoms were anomalies of the tooth formation, dysgnathia, changes in number of the teeth, and malocclusions. The OHIP mean values of the five resulting symptom clusters ranged from 15.1 to 19.9, which is very high compared to the general population in Germany, which has a mean value of 4.09. Discussion: All investigated symptoms show a negative association with OHRQoL, but the strongest were for symptoms of the oral mucosa and periodontal diseases. All the symptoms described in this cluster analysis can lead to considerably higher mean values of the OHIP total score among people with rare disease and thus to worse OHRQoL than reported in the general population.