The classic view that secondary constituents are waste products in plants has been replaced by one in which their value is assumed to be as a protection against herbivorous and microbial attack. However, secondary pathways may still be physiologically important as a means of channelling and storing carbon compounds, accumulated from photosynthesis, during periods when nitrogen is limiting or whenever leaf growth is curtailed. Large increases in the amount of secondary metabolites can occur in stressed plants and those subject to mechanical damage or that caused by insects.

In order to establish a protective role for a given metabolite, it is necessary to monitor concentrations over the life cycle of the plant, to survey plant populations, to determine specific localization within tissues and to carry out bioassays against insects and microorganisms. Synergy between toxins of the same class or of different classes is likely. Changes in secondary chemistry may also occur during ontogeny, and protection may be restricted to the most vulnerable plant organs. Finally, toxins may vary indiscriminately in their distribution within the plant or within populations and still provide protection.