Background: Although leaf herbivory-induced changes in allocation of recently assimilated carbon between the shoot and below-ground tissues have been described in several species, it is still unclear which part of the root system is affected by resource allocation changes and which signalling pathways are involved. We investigated carbon partitioning in root tissues following wounding and simulated leaf herbivory in young Nicotiana attenuata plants. Results: Using 2-deoxy-2-[18F]fluoro-D-glucose ([18F]FDG), which was incorporated into disaccharides in planta, we found that simulated herbivory reduced carbon partitioning specifically to the root tips in wild type plants. In jasmonate (JA) signalling-deficient COI1 plants, the wound-induced allocation of [18F]FDG to the roots was decreased, while more [18F]FDG was transported to young leaves, demonstrating an important role of the JA pathway in regulating the wound-induced carbon partitioning between shoots and roots. Conclusions: Our data highlight the use of [18F]FDG to study stress-induced carbon allocation responses in plants and indicate an important role of the JA pathway in regulating wound-induced shoot to root signalling.