ObjectivesTo determine and compare pulp volume, dentin mineral density, presence of microcracks, pulp stones, and accessory canals, as well as their localizations in root regions for hypomineralized and healthy teeth. DesignThis study included 60 extracted permanent molar teeth, categorized into hypomineralized and healthy groups (n = 30 each). The hypomineralized group comprised molar teeth with limited white, yellow, or brown opacities, post-eruptive breakdown, or extensive restoration or crown damage. The healthy group included caries-free molar teeth without these characteristics. Using 3D micro-computed tomography images pulp volume, dentin mineral density, and the presence and locations of microcracks, pulp stones, and accessory canals were determined for each group. Statistical analyses were conducted using Independent T-test and Chi-square test, with significance set at p < 0.05. ResultsThere was no statistically significant difference between the groups regarding pulp volume and microcracks (p ≥ 0.05). The number of accessory canals was significantly greater in the cervical (p = 0.011; p < 0.05) and middle (p = 0.010; p < 0.05) regions of the hypomineralized teeth than healthy teeth. Dentin mineral density was statistically higher in the apical, middle, and cervical root regions (p < 0.001; p < 0.05); however, the number of pulp stones was found to be greater in the cervical regions of healthy teeth compared with those with hypomineralization (p = 0.026; p < 0.05). ConclusionThere were lower dentin mineral density measurements, a decreased number of pulp stones in the cervical region, and a greater number of accessory canals in the middle and cervical regions of hypomineralized teeth compared with healthy teeth.