Radioiodine-131 (I-131) is an essential therapy for patients with differentiated thyroid carcinomas (DTC). Generally, I-131 is safe and well tolerated, but patients may present early or late complications in the oral and maxillofacial areas. Thus, the aim of this study was to evaluate in-vitro, the alteration of enamel and dentin after I-131 exposure using histopathological assessment, scanning electron microscopy (SEM) and atomic force microscopy (AFM). For I-131 irradiation, an in-vitro protocol was used that simulates the procedure for irradiation therapy performed for patients with DTCs. A total of 42 teeth were divided into seven groups (n = 6) and irradiated as follows: control, irradiation groups (3, 6, 12, 36, 48 h, 8 days). Histological changes were observed at 48 h (enamel surface with multifocal and irregular areas) and at 8 days (enamel surface with multiple, very deep, delimited cavities). SEM imaging revealed the enamel destruction progresses along with the treatment time increasing. The alterations are extended into the enamel depth and the dislocated hydroxyapatite debris is overwhelming. The enamel-dentine interface shows small gaps after 6 h and a very well developed valley after 12 h; the interface microstructure resulted after 8 days is deeply altered. The AFM imaging shows that I-131 affects the protein bond between hydroxyapatite nano-crystals causing loss of cohesion, which leads to significant increasing of nano-particles diameter after 6 h. In conclusion, both enamel and dentin appear to be altered between 12 and 48 h and after 8 days of treatment are extended in depth.