We carry out the spectral analysis of enamel, enamel-dentin junction, and dentin of human teeth at the stage of connective tissue dysplasia and without it. It is established that in the case of connective tissue dysplasia in the hard tissues of teeth there is a clear heterogeneity of spectra. In the group with connective tissue dysplasia the maximum changes of IR spectra are observed in collagen and non-collagen proteins of the organic matrix of enamel and dentin. For the group without connective tissue dysplasia the greater uniformity is observed in dentin. The biochemical abnormalities detected in the dentin of the lower “wisdom” teeth can be explained by dysplastic collagen formation disorders in the dental hard tissues, which leads to marked shifts in the enamel layer under the aggressive action of the oral fluid. In the group without connective tissue dysplasia the imbalance in the structure of the protein matrix of tooth enamel is related only to the mineralizing effect of the oral fluid on it.