Human dental tissues consist of inorganic constituents (mainly crystallites of hydroxyapatite, HAp) and organic matrix. In addition, synthetic HAp powders are frequently used in medical and chemical applications. Insights into the ultrastructural alterations of skeletal hard tissues exposed to thermal treatment are crucial for the estimation of temperature of exposure in forensic and archaeological studies. However, at present, only limited data exist on the heat-induced structural alterations of human dental tissues. In this paper, advanced non-destructive small- and wide angle X-ray scattering (SAXS/WAXS) synchrotron techniques were used to investigate the in situ ultrastructural alterations in thermally treated human dental tissues and synthetic HAp powders. The crystallographic properties were probed by WAXS, whereas HAp grain size distribution changes were evaluated by SAXS. The results demonstrate the important role of the organic matrix that binds together the HAp crystallites in responding to heat exposure. This is highlighted by the difference in the thermal behaviour between human dental tissues and synthetic HAp powders. The X-ray analysis results are supported by thermogravimetric analysis. The results concerning the HAp crystalline architecture in natural and synthetic HAp powders provide a reliable basis for deducing the heating history for dental tissues in the forensic and archaeological context, and the foundation for further development and optimization of biomimetic material design.