Teeth are unique and complex anatomical organs that can provide relevant data about a person's health, and play an important role in forensic medicine. Teeth are exposed to food, drinks, and the microbiota of the oral cavity; therefore, they have developed a high resistance to localized demineralization. Nevertheless, the continuous demineralization–remineralization cycle present in the oral environment can be influenced by stress, medication, mineralization agents, and other factors such as individual habits, especially diet. In this study, based on attenuated total reflectance Fourier-transform infrared spectroscopy (ATR-FTIR) spectra from tooth samples of 36 patients, several parameters were estimated: the crystallinity index (CI), the phosphate/amide I ratio, and the carbonate/phosphate ratio. In addition, in eight representative samples (six of the root of the tooth and two of the enamel area of the crown), additional characterization by X-ray powder diffraction (XRPD), scanning electron microscopy (SEM) and energy-dispersive X-ray spectroscopy (EDS) was conducted. From the FTIR data, it was observed that the highest CI values were found in patients who smoked. Further, in both root and crown samples, the intensity of the absorption band corresponding to PO43- increased in patients undergoing treatment with psychotherapeutic drugs. On the other hand, the intensity of the absorption band of the amide I group decreased with medical treatment and with the patient's biological age. Moreover, it was found that the remineralization process was more active in enamel than in the root due to direct contact with saliva. Regarding the results obtained from the X-ray powder diffractograms, exposure to psychotherapeutic drugs affected the definition of the peaks corresponding to hydroxyapatite, both in the crown and root samples. Concerning SEM results, qualitative differences in the stratification process in demineralized surfaces were observed, and EDS analyses showed some differences in the Ca/P ratio between pathological samples and control ones, but without clear patterns. The above techniques, in particular ATR-FTIR, showed promise for the investigation of the effect of changes produced in the hydroxyapatite structure in teeth and, consequently, to determine possible strategies in the diagnostic protocol.