Gas chromatography (GC)-based metabolomics technologies were applied for quality control of Angelicae Radix, an herbal medicine commonly used in Japan and China. Since Angelica roots are priced and graded differently based on their species and cultivation area, there is a need for a simple and reproducible method to discriminate Angelica roots. Here, we used GC-MS profiling data to construct a discrimination method for species and cultivation area of A. Radix. Seventy-six primary metabolites were identified. The quality factors of A. Radix were successfully classified using metabolic profiling and the orthogonal projections to latent structures-discriminant analysis (OPLS-DA) technique. Sorbitol and a glucose/4-aminobutyric acid combination were chosen as bio-markers from S-plot of OPLS-DA. Application of these selected bio-markers to a more practical and cost-efficient system, namely gas chromatography-flame ionization detector (GC-FID) system were also assessed. As a result, the same separations of sorbitol, glucose and 4-aminobutyric acid in box plots were obtained from GC-FID data. Our results demonstrate that GC-based metabolic markers can be readily applied for the establishment of a practical quality control method for A. Radix. (c) 2012, The Society for Biotechnology, Japan. All rights reserved.