The transition from a pathway-centred view of plant metabolism to a network-wide perspective is still incomplete. Further progress in this direction requires tools to facilitate the structural description of the network on the basis of fully annotated genomes, techniques for modelling the properties of the network, and experimental methods for constraining the models and verifying their outputs. It also requires a focus on metabolic flux as the key to understanding the regulation of metabolic activity and the relationship between the inputs and outputs of the network. Progress is being made on several fronts and this Special Issue on ‘Pathways and fluxes: exploring the plant metabolic network’ describes current developments in the genomic reconstruction of metabolic networks, the application of flux-balance analysis to such networks, kinetic modelling, and both steady-state-and non-steady state isotope-based measurements of multiple fluxes in the network of central carbon metabolism. The papers also highlight insights that can be obtained from pathway analysis, particularly in relation to the thermodynamic and kinetic efficiency of the predicted and observed flux distributions.