Metabolomics, the comprehensive and global analysis of diverse metabolites produced in cells and organisms, has greatly expanded metabolite fingerprinting and profiling as well as the selection and identification of marker metabolites. The methodology typically employs multivariate analysis to statistically process the massive amount of analytical chemistry data resulting from high-throughput and simultaneous metabolite analysis. Although the technology of plant metabolomics has mainly developed with other post-genomics in systems biology and functional genomics, it is independently applied to the evaluation of the qualities of medicinal plants, based on the diversity of metabolite fingerprints resulting from multivariate analysis of non-targeted or widely targeted metabolite analysis. One advantage of applying metabolomics is that medicinal plants are evaluated based not only on the limited number of metabolites that are pharmacologically important chemicals, but also on the fingerprints of minor metabolites and bioactive chemicals. In particular, score plot and loading plot analyses e.g. principal component analysis (PCA), partial-least-squares discriminant analysis (PLS-DA), and discrimination map analysis such as batch-learning self-organizing map (BL-SOM) analysis, are often employed for the reduction of a metabolite fingerprint and the classification of analyzed samples. Based on recent studies, we now understand that metabolomics can be an effective approach for comprehensive evaluation of the qualities of medicinal plants. In this review, we describe practical cases in which metabolomic study was performed on medicinal plants, and discuss the utility of metabolomics for this research field, with focus on multivariate analysis.