Primary carbohydrate metabolism plays an essential role in the growth and development of plants. Despite the fact that most of the intermediary steps in the metabolic pathways involved are known, knowledge about the genetic regulation of this complex biochemical network is limited. We have recently shown that exploring natural variation is an efficient approach to reveal genetic regulation at various stages along the path from genotype to phenotype.1 In this study genetic analyses were performed at the levels of gene expression, activity of a subset of enzymes involved in carbohydrate metabolism and abundance of the metabolites involved in the reactions catalyzed by these enzymes. Although a strong correlation was observed between the different entities analyzed, specific regulation of individual components could also be observed at different levels. These results show that the genetic regulation of plant carbohydrate metabolism is highly complex which advocates the application of multi-disciplinary approaches to disentangle the various interacting regulatory modes.