Objectives: The aim of this study was to perform a comparative analysis of the ultrastructural and chemical composition of sialoliths, tonsilloliths, and antroliths and to describe their growth pattern. Materials and Methods: We obtained 19 specimens from 18 patients and classified the specimens into three groups: sialolith (A), tonsillolith (B), and antrolith (C). The peripheral, middle, and core regions of the specimens were examined in detail by histology, micro-computed tomography (micro-CT), scanning electron microscopy (SEM), energy dispersive X-ray spectroscopy, and transmission electron microscopy (TEM). Results: In the micro-CT, group A showed alternating radiodense and radiolucent layers, while group B had a homogeneous structure. Group C specimens revealed a compact homogeneous structure. Histopathologically, group A showed a laminated, teardrop-shaped, globular structure. Group B demonstrated degrees of immature calcification of organic and inorganic materials. In group C, the lesion was not encapsulated and showed a homogeneous lamellar bone structure. SEM revealed that group A showed distinct three layers: a peripheral multilayer zone, intermediate compact zone, and the central nidus area; groups B and C did not show these layers. The main elemental components of sialoliths were O, C, Ca, N, Cu, P, Zn, Si, Zr, F, Na, and Mg. In group B, a small amount of Fe was found in the peripheral region. Group C had a shorter component list: Ca, C, O, P, F, N, Si, Na, and Mg. TEM analysis of group A showed globular structures undergoing intra-vesicular calcification. In group B, bacteria were present in the middle layer. In the outer layer of the group C antrolith, an osteoblastic rimming was observed. Conclusion: Sialoliths had distinct three layers: a peripheral multilayer zone, an intermediate compact zone and the central nidus area, while the tonsillolith and antrolith specimens lacked distinct layers and a core.