Objective As SELDI-TOF-MS (Surface Enhanced Laser Desorption/Ionization Time of Flight Mass Spectrometry) has been broadly used to screen biomarkers for a variety of diseases, the identification and validation of the revealed biomarkers requires more focused attention.Method In this paper, the serum samples from 60 cholangiocarcinoma, 146 lung cancer, 65 LGC and 58 LPC, 49 benign diseases of hepatobiliary and 53 normal individuals were analyzed by SELDI-TOF-MS. Results Among a set of proteins automatically selected as specific biomarkers by Biomarker Wizard software, three protein peaks, with molecular weights of 13. 71 × 103 , 13.83 × 103 and 13. 99 ×103 , were found significantly decreased in cholangiocarcinoma samples. The candidate biomarkers obtained from Tricine-SDS-PAGE gel bands by matching the molecular weight with peaks on CM10 chips were identified by Mass spectrometry as the native transthyretin(native TTR),cysTTR and glutTTR.These preliminary results were further proven by immunoprecipitation using commercial TTR antibodies. This allowed us to re-measure the TTR levels in all the groups more simply by ELISA assay. It showed a firm consistency between ELISA and SELDI analysis. In addition, while TTR levels in cholangiocarcinoma were found to be lower than those in normal healthy controls, TTR levels in benign diseases of the hepatobiliary system were found to be higher than those in healthy controls.Conclusion TTR could be a biomarker that better discriminates cholangiocarcinoma patients from the benign diseases compared to other biomarkers presently available.