Background: Ehlers-Danlos syndrome (EDS) is a hereditary disorder that affects the connective tissue and collagen structures in the body characterised by joint hypermobility, skin hyperextensibility and tissue fragility. Objective: The aim of the study was to investigate the oro-dental characteristics including measurements of tooth size of 26 patients with hypermobile EDS (hEDS), differentiated by a genetic test, compared to 39 healthy controls. Methods: Interview, clinical and radiological examination on panoramic radiograph and cone-beam computed tomographic (CBCT) scan were performed. Statistical analyses included Fisher's exact test, paired t test and multiple logistic and linear models adjusted for age and gender. Results: The experience of xerostomia (P = 0.039), local anaesthetic insufficiency (P < 0.001) and tooth extraction complications (P < 0.003) were significantly higher in hEDS compared to controls. The debris index was significantly higher in hEDS (P < 0.001), and the distance between the cement-enamel junction (CEJ) and the bone level on the upper left first incisor and molar and the lower right first molar was significantly larger in hEDS compared to controls (P = 0.021, P = 0.024, P = 0.021, respectively). The crown heights of the upper and lower first incisors were significantly smaller (P = 0.001, P = 0.003, P = 0.002, P < 0.001, respectively) in hEDS compared to controls. When adjusting for debris index, only the distance between CEJ and the marginal bone level on the upper left and lower right molar was associated with hEDS. Conclusion: The results indicate that xerostomia, resistance to local anaesthesia, tooth extraction complications, poor oral hygiene, larger distance between CEJ and marginal bone level and small crown heights can be found in patients with hEDS.