The purpose of this study is to establish the cell and subcellular basis for the diagnosis of colorectal cancer by researching the FTIR( Fourier transform infrared spectra) of the normal tissue (30 cases) and cell line (SW 620), normal nuclei and malignant nucleus with Fourier transform infrared spectrum technology. The results of the peak position and the relative intensity obtained by statistical analysis indicate that the bands at 2 925, 1 240 and 1 085 cm-1 shifted toward higher wavenumber (p<0.05) in the FTIR spectra of cell lines (SW 620) and malignant nucleus. The 1 400 cm-1 band shifted toward lower wave number (p<0.05). The relative intensity ratios of I1 650/I1 460, I1 400/I1 460 and I1 240/I1 460 increased in the FTIR spectra of cell lines (SW 620) compared with normal tissue (p<0.05), but inversely, I1 740/I1 460 decreased significantly (p<0.01). The relative intensity ratios of I1 650/I1 460, I1 400/I1 460 and I1 240/I1 460 also increased in the FTIR spectra of the malignant nucleus. The above statistic differences are the basis for diagnosing colorectum cancer by FTIR spectroscopy.