Thirty thyroid samples of normal and abnormal tissues were analyzed by infrared and confocal Raman Spectroscopy. We studied the Amide I (1,720–1,580 cm−1) spectral region in order to determine different components of the proteins' secondary structure in the samples. Peak positions of the Amide I bands were determined using the second derivative and Fourier self‐deconvolution of infrared and Raman spectra. We obtained band areas corresponding to β‐turn, 310‐helix, α‐helix, β‐sheet, β‐turns, and side chains for the infrared and confocal Raman spectra by Gaussian fitting. Using the second derivative of the infrared and Raman spectra, we demonstrated the consistency of the vibrational assignments because compounds of low symmetry without an inversion center present coincident bands that differ only in intensity; hence, the infrared procedures to identify and assign the bands of the proteins' secondary structure in the Raman spectra are valid. The results obtained are supported by vibrational theory and indicate that infrared and confocal Raman spectroscopy are important, useful, and fast tools to identify changes in the proteins' secondary structure in normal tissues, goiter, and follicular and papillary thyroid carcinomas.