The primary and secondary metabolites found in plant cells are the final recipients of biological information flow. In turn, their levels can influence gene expression and protein stability. Qualitative and quantitative measurements of these metabolites reflect the cellular state under defined conditions, and yield critical insights into the cellular processes that control the biochemical phenotype of the cell, tissue or whole organism. Metabolomics differs from traditional targeted phytochemical analysis in various fundamental aspects; for example, it is a data-driven approach with predictive power that aims to assess all measurable metabolites without any pre-conception or pre-selection. As such, metabolomics is providing new dimensions in the study of systems biology, enabling the in-depth understanding of the intra- and extracellular interactions of plant cells. Metabolomics is also developing into a valuable tool that can be used to monitor and assess gene function, and to characterise post-genomic processes from a broad perspective. Here, we give an overview of the fundamental analytical technologies and subsequent multivariate data analyses involved in plant metabolomics as a research tool to study various aspects of plant biology.