The diagnosis of thyroid pathologies is usually made by cytologic analysis of the fine needle aspiration (FNA) material. However, this procedure has a low sensitivity at times, presenting a variation of 2–37%. The application of optical spectroscopy in the characterization of alterations could result in the development of a minimally invasive and non-destructive method for the diagnosis of thyroid diseases. Thus, the objective of this work was to study the biochemical alterations of tissues and hormones (T3 and T4) of the thyroid gland by means of molecular vibrations probed by FT-Raman spectroscopy. Through the discriminative linear analysis of the Raman spectra of the tissue, it was possible to establish (in percentages) the correct classification index among the groups: goitre adjacent tissue, goitre nodular region, follicular adenoma, follicular carcinoma and papillary carcinoma. As a result of the comparison between the groups goitre adjacent tissue versus goitre nodular region, an index of 58.3% of correct classification was obtained; this percentage was considered low, and it was not possible to distinguish the Raman spectra of these groups. Between goitre (nodular region and adjacent tissue) versus papillary carcinoma, the index of correct classification was 64.9%, which was considered good. A relevant result was obtained in the analysis of the benign tissues (goitre and follicular adenoma) versus malignant tissues (papillary and follicular carcinomas), for which the index was 72.5% and considered good. It was also possible, by means of visual observation, to find similar vibrational modes in the hormones and pathologic tissues. In conclusion, some biochemical alterations, represented by the FT-Ramanspectra, were identified that could possibly be used to classify histologic groups of the thyroid. However, more studies are necessary due to the difficulty in setting a standard for pathologic groups.