The developmental regulation and organ-specific expression of shikimate dehydrogenase was studied in seedlings of Capsicum annuum L. during their early development. The results obtained suggest that there is both a developmental regulation and an organ-specific expression of shikimate dehydrogenase in seedlings of C. annuum, seen mainly in the cotyledons. For example, shikimate dehydrogenase isoenzyme 3 was differentially expressed in cotyledons, but not at all in roots or hypocotyls. When the amounts of shikimate dehydrogenase were compared with the end-products of the shikimate pathway, chlorogenic acid and lignins, it was observed that the fall in shikimate dehydrogenase activity in cotyledons coincided with a decrease in the concentrations of phenolics during primary leaf development. However, this did not seem to be the case with the hypocotyls, where the fall in phenolics was not related to the amount of shikimate dehydrogenase but rather to an increase in lignin deposition, supporting the view that chlorogenic acid might act as a precursor of the aromatic moiety of cinnamoyl alcohols during cell wall lignification.