Metabolomics, which aims at the comprehensive and quantitative analysis of wide arrays of metabolites in biological samples, is playing an increasingly important role in plant science. Various biological issues have been successfully studied by this holistic approach that includes global metabolite composition assessment, mutant characterization, taxonomy, developmental processes, stress response, interaction with environment, quality control assessment and mode of action of herbal medicine. This review summarizes the main mass spectrometry methods used for performing these studies and discusses the potential, but also the current limitations of the various approaches. The intention is not to cover exhaustively the field, which has considerably grown over about one decade, but to give a brief insight into the methods commonly employed and discuss some applications that reveal the potential of metabolomics in phytochemistry and systems biology.