Tissue analysis by Fourier transform infrared (FTIR) imaging can determine the biodistribution of molecules,without pre-analytical modification. We aimed to study the infrared spectroscopic changes of α-helical proteinsat post-traumatic epileptic (PTE) foci by FTIR. FITR mapping was applied to detect α-helical proteins in ratbrain tissue samples with post-traumatic epilepsy. Histological examination of brain sections showed that therat model of PTE was successfully established. At the PTE foci, high α-helical absorption regions wereevident, where the color difference and absorption were significantly different from those in the low-absorptionregions. This provided a distinctive and characteristic pattern at the site of lesions. The use of FTIR imagingmeans that it is possible to measure the molecular structural changes resulting from PTE pathologies in tissues,providing a novel adjunct to conventional pathological diagnostic techniques.