Authentication of sandalwood crude drugs available in Thai traditional drugstores was investigated by gas chromatography-mass spectroscopy combined with chemometric methods. Three species of Santalum were discriminated based on GC-MS fingerprint analysis using similarity analysis, cluster analysis and principal component analysis. The major common peaks of the chromatogram were identified by Kovats Index (KI) calculation and by comparing their mass spectra to those in libraries database. All data were compared with those of authentic samples. Most crude drugs were identified as S. spicatum, whereas only some samples were S. album and S. lanceolatum. The result of this study concluded that S. album, the correct species mentioned for medical use of sandalwood, was currently substituted with other Santalum species.