The availability of sequence data is contributing immensely to the development of gene-expression resources, in parallel to these advances, several methods have been established for systematic analysis of metabolite composition. In this chapter, we illustrate the utility of parallel transcript and metabolic profiling analysis to study metabolic regulation during the day/night cycle. Recently we presented a gas chromatography-mass spectrometry-based metabolic profiling protocol, alongside spectrophotometric techniques, to follow changes in a broad range of potato leaf metabolites throughout the day/night cycle (Urbanczyk-Wochniak et al., 2005). In tandem, we profiled transcript levels using both a custom array containing approximately 2,500 cDNA clones representing predominantly transcripts involved in plant metabolism, and commercially available arrays containing approximately 12,000 cDNA clones that gave coverage of transcript levels over a broader functional range. The levels of many metabolites and transcripts varied during the day/night cycle. Whilst a large number of the differences might be expected based on earlier data, several novel changes were seen. Here we present novel description of changes in metabolites and genes associated with secondary metabolism. Profiling of diurnal patterns of metabolite and transcript abundance in potato leaves suggests that specific sets of metabolic pathway are strongly transcriptionally regulated, but revealed that the majority of the metabolic network is primarily under post-transcriptional control.