A total of 184 specimens from gastroscopy were studied using Fourier transform infrared (FTIR) spectroscopy. The spectra of small-sized gastric endoscope samples with high quality were measured using the modified FTIR spectrometer with a MCT detector. The results show that the spectra of chronic superficial gastritis are similar to those of the normal block tissue in our previous study. But there are significant differences in band location and relative intensity between the spectra of chronic superficial gastritis and those of normal gastric tissues. Similarly, the differences exist in the spectra of chronic atrophic gastritis and those of malignant gastric tissues. In addition, the subtraction technique can provide more information to identify well the gastric samples of chronic atrophic gastritis, superficial gastritis and gastric cancer from endoscope the detection. These results indicate that FTIR spectroscopy exhibits potential to diagnose the gastric samples from gastroscopy.