(1) Objectives: The aim of our study was to investigate the anatomical features of lower third molar and its adjacent anatomical connections in type I Osteogenesis Imperfecta (OI) patients through cone beam computed tomography (cbct). (2) Methods: The study was conducted among 25 patients, 13 patients with type I OI and 12 control patients (individuals with no disorders and no treatment); average age was 15.44 ± 2.06, 23 third molar germs for each group. The germs have been compared to the parameters using the Mann-Whitney test. A chi-square test was also used to investigate the correlation between the status case/control and tooth development stage. (3) Results: Mann-Whitney test showed significant differences between cases and controls: diameter of the tooth germ in toto (U = 93.5; p < 0.001), tooth development stage, (U = 145; p < 0.01), roots length (U = 44.5; p < 0.01), cementoenamel junction diameter (U = 157.5; p < 0.05), size of the pulp chamber (U = 95.5; p < 0.05). Type I OI is not associated with the relationship between the germ of mandibular third molar and alveolar canal on axial plane (χ2 = 4.095; p = 0.129), and parasagittal (χ2 = 4.800; p = 0.091). The association between type I OI and relationship with the germ of mandibular third molar and alveolar canal on the coronal plane has been significant (χ2 = 9.778; p < 0.05) as the perforation of the lingual cortical bone in the region of mandibular third molar tooth germ (χ2 = 11.189; p < 0.01). (4) Conclusions: The results confirm the cbct accuracy in the evaluation of bone density in type I OI patients giving also the opportunity to study the tridimensional anatomy of germs and the adjacent anatomical structures in order to avoid any perioperative complications.