Benzo[a]pyrene (B[a]P) and 2,2′,4,4′-tetrabromodiphenyl ether (BDE-47) are widespread environmental pollutants and can destroy thyroid function. We assessed the biochemical changes in the thyroid tissue of rats exposed to B[a]P and BDE-47 using attenuated total reflection Fourier-transform infrared spectroscopy combined with support vector machine(SVM). After B[a]P and BDE-47 treatment in rats, the structure of thyroid follicles was destroyed and epithelial cells were necrotic, indicating that B[a]P and BDE-47 may lead to changes of the thyroid morphology of the rats. These damages are mainly related to C�O stretch vibrations of lipids (1743 cm −1 ), as well as the secondary structure of proteins [amide I (1645 cm −1 ) and amide II (1550 cm −1 )], and carbohydrates [C−OH (1138 cm −1 ), C−O (1106 cm −1 , 1049 cm −1 , 991 cm −1 ), C−C (1106 cm −1 ) stretching] and collagen (phosphodiester stretching at 922 cm −1 ) vibration modes. When SVM was used for classification, there was a substantial separation between the control and the exposure groups (accuracy = 96%; sensitivity = 98%; specificity = 87%), and there was also a major separation between the exposed groups (accuracy = 93%; sensitivity = 94%; and specificity = 92%).