Background Fourier transform infrared spectroscopy (FT-IR) combined with chemometrics discriminant analysis technology could improve diagnosis. The present study aimed to evaluate the effects of FT-IR on malignant colon tissue samples in diagnosis of colon cancer.Methods Principal component analysis (PCA) and support vector machine classification were used to discriminate FT-IR spectra from malignant and normal tissue. Colon tissues samples from 85 patients were used to demonstrate the procedure.Results For this set of colon spectral data, the sensitivity and specificity of the support vector machine (SVM)classification were found both higher than 90%.Conclusions FT-IR provided important information about cancerous tissue, which could be used to discriminate malignant from normal tissues. The combination of PCA and SVM classification indicated that FT-IR has a potential clinical application in diagnosis of colon cancer.