A comparative FTIR study was undertaken between ATR (attenuated total reflection) and infrared microscopy on their application to measuring the same tissue for cancer diagnosis. The measurements showed that the coincidence of pathological diagnosis with ATR is higher than that of microscopy FTIR method. The result indicated that the measured area of tumor tissue is critical. The area for microscopy measurement is approximately 250 microm2, it reflects the heterogeneity of the tissue. However, the ATR measurement provides more information of malignant tissue for the measured area is 1.9 x 10(5) times than microscopy. Therefore, ATR exhibit the high accuracy in cancer detection for clinical application.