The aim of this study was to explore the possibility of applying Fourier transform infrared(FTIR) spectroscopy as a medical diagnostic tool based on a neural network classifier for detecting and classifying cholangiocarcinoma. A total of 51 cases of bile duct tissues were obtained and later characterized by FTIR spectroscopy prior to pathological diagnosis. The criteria for classification included 30 parameters for each FTIR spectra, including peak position(P), intensity(I) and full width at half-maximum(FWHM), were measured, calculated and subsequently compared against the normal and cancer groups. The FTIR spectra were classified by the radial basis function(RBF) network model. For establishing the RBF, 23 cases were used to train the RBF classifier, and 28 cases were applied to validate the model. Using the RFB model, nine parameters were observed to be pronouncedly different between cancerous and normal tissue, including I1640, I1550, I1460, I1400, I1250, I1120, I1080, I1040 and P1040. In the RBF training classification, the accuracy, sensitivity, and specificity of diagnosis were 82.6%, 80.0%, and 84.6%, respectively. While validating the classification, the accuracy, sensitivity, and specificity of diagnosis were 78.6%, 75.0%, and 81.2%, respectively. The results suggest that FTIR spectroscopy combined with neural network classifier could be applied as a medical diagnostic tool in cholangiocarcinoma diagnosis.