In the postgenomic era, metabolomics is expected to be the newest useful omics science for functional genomics. However, in plant science, the present metabolomics technology cannot be considered a universal tool to perfectly elucidate perturbations imposed on sample plants although this is desired by plant physiologists. Despite it being an immature technology, metabolomics has already been used as a powerful tool for precise phenotyping, particularly for industrial application. Metabolomics is the best technology for the analysis of large mutant or transgenic libraries of model experimental plants, such as Arabidopsis, rice, etc. Here, we review the applications and technical problems of metabolomics. We also suggest the potential of metabolomics for plant post-genomic science.