Fourier transform infrared spectroscopy (FTIR) was applied to study the biochemical changes in the radiation damaged mouse thymus which increased with radiation dose and provided a new method for the estimation of the radiation dose of radiation damaged patients. The results demonstrated that with the dose increasing, the peak positions like 1 550, 1 400, 1 400 and 1 640 cm-1 at the dose of 2, 3 and 5 Gy showed some difference, and there was obvious variance in the intensity: (1) The intensity ratio of 1 085 to 1 236 cm-1 related to nucleic acid tended to decrease. (2) The intensity ratio of 1 640/1 550 decreased. (3) The intensity at 2 958, 2 925, 1 460 and 1 400 cm-1 showed no significant difference. The results suggest that it may be possible for FTIR to become an effective method to estimate the radiation dose in clinic.