Thyroid follicular nodules are quite common in the population, however only a small proportion is malignant. Thyroid cancer differs from adenoma by features of cellular atypia, angioinvasiveness and possibility of metastasis via blood vessels mainly in the lungs and bones. Pathomorphological examination of the postoperative material plays a significant role in the diagnosis of cystic thyroid lesions. De facto, there is no possibility to determine with certainty whether the lesion is benign or malignant before surgery, therefore new methods are being sought to meet clinical needs. The study aimed to investigate if Fourier-transform infrared spectroscopy (FTIR) spectroscopy and Raman spectroscopy combined with multidimensional analysis can be a useful tool in distinguishing between thyroid adenomas and carcinomas. The obtained results indicate quantitative and qualitative alterations within proteins and fats derived from patients' tissues samples. Raman spectroscopy additionally shows significant changes in the amount of tissue collagen due to the pathogenic process. In the spectra of the second FTIR derivative, shifts of vibrations corresponding to the β-sheet and α-helix structure are observed towards the lower rates of wave numbers in the case of neoplastic tissues. Using the leave-one-out cross-validation, sensitivity and specificity calculated with Principal Component Analysis-Linear Discriminant Analysis (PCA-LDA) clearly shows the possibility to distinguish between pathologically changed and normal thyroid tissue as well as differentiate follicular thyroid adenoma (FTA) from widely invasive follicular thyroid carcinoma (WI-FTC) tissues.