Tomato fruits (Solanum lycopersicum L.) accumulate flavonoids in their cuticle and epidermal cells during ripening. These flavonoids come from de novo biosynthesis due to a significant increase in chalcone synthase (CHS) activity during ripening. Virus-induced gene silencing (VIGS) of tomato fruits have been used to down-regulate SlCHS expression during ripening and analyze the effects at the epidermal and cuticle level. Besides the expected change in fruit color due to a lack of flavonoids incorporated to the cuticle, several other modifications such as a decrease in the amount of cutin and polysaccharides were observed. These indicate a role for either flavonoids or CHS in the alteration of the expression levels of some genes involved in cuticle biosynthesis. Moreover, a negative interaction between the 2 cuticle components, flavonoids and waxes, suggests a relationship between these 2 metabolic pathways.