Secondary compounds serve both endogenous and exogenous functions in higher plants because they are involved in plant growth and development as well as intraspecies and interspecies interactions. Documentation of the effects of pesticides on secondary compound biosynthesis in higher plants is increasing. While several herbicides have been reported to reduce levels of secondary compounds by non‐specific mechanisms, a few herbicides, such as alachlor and glyphosate, directly affect specific biosynthetic steps. Alachlor reduces flavonoid synthesis at a step late in the biosynthetic pathway, and glyphosate blocks synthesis of all cinnamate derivatives by inhibiting 5‐enolpyruvyl shikimate‐3‐phosphate (EPSP) synthase. Inhibition of EPSP synthase also leads to the accumulation of high levels of shikimate, benzoic acids and benzoic acid derivatives. The sulfonylureas and p‐nitro‐substituted diphenylether (DPE) herbicides can cause increases in the level of cinnamatederived phenolic compounds and the DPEs can cause dramatic increases in terpenoid stress metabolites. Certain fungicides are thought to act through enhancing the capacity of plants to produce phytoalexins. These and other data suggest that sublethal effects of pesticides on target and non‐target plants can significantly affect agricultural ecosystems by altering the synthesis of compounds important in inter‐ and intraspecies interactions.