Incomplete knowledge of biochemical pathways makes the holistic description of plant metabolism a non-trivial undertaking. Sensitive analytical platforms, which are capable of accurately quantifying the levels of the various molecular entities of the cell, can assist in tackling this task. However, the ever-increasing amount of high-throughput data, often from multiple technologies, requires significant computational efforts for integrative analysis. Here we introduce the application of network analysis to study plant metabolism and describe the construction and analysis of correlation-based networks from (time-resolved) metabolomics data. By investigating the interactions between metabolites, network analysis can help to interpret complex datasets through the identification of key network components. The relationship between structural and biological roles of network components can be evaluated and employed to aid metabolic engineering. © 2012 Elsevier Ltd.