The objective of this study was to characterize natal and neonatal teeth using micro-computed tomography. A total of 4 natal and 11 neonatal teeth were used for the analysis. The reconstructed scans were assessed for the maximum enamel/dentin thickness and mineral density (MD). The scanned specimens were 3D reconstructed to qualitatively determine the surface topography. The dentin thickness was two-fold greater than enamel thickness for both natal and neonatal teeth (p < 0.05). The cervical third enamel MD remained undetermined in natal and neonatal teeth. The dentin MD at the cervical third for neonatal teeth was significantly lower than the incisal and middle third dentin (p < 0.05). Similarly, the dentin MD at the cervical third of neonatal teeth was significantly lower than the cervical third dentin MD of natal teeth (p < 0.05). Our qualitative analysis suggests that the cervical thirds of both natal and neonatal teeth are peculiar of an anomalous structure, with neonatal teeth showing an irregular outline. Under the conditions of the present study, it can be concluded that the neonatal teeth studied exhibited a distinguishable aberrant structure compared to the natal teeth. Therefore, the natal teeth unfold as a more organized, three-dimensional structure compared to the neonatal teeth.