Secondary metabolites can be classified on the basis of chemical structure (for example, having rings, containing a sugar), composition (containing nitrogen or not), their solubility in various solvents, or the pathway by which they are synthesized (e.g., phenylpropanoid, which produces tannins). A simple classification includes three main groups: the terpenes (made from mevalonic acid, composed almost entirely of carbon and hydrogen), phenolics (made from simple sugars, containing benzene rings, hydrogen, and oxygen), and nitrogen-containing compounds (extremely diverse, may also contain sulfur).

The apparent lack of primary function in the plant, combined with the observation that many secondary metabolites have specific negative impacts on other organisms such as herbivores and pathogens, leads to the hypothesis that they have evolved because of their protective value. Many secondary metabolites are toxic or repellant to herbivores and microbes and help defend plants producing them. Production increases when a plant is attacked by herbivores or pathogens. Some compounds are released into the air when plants are attacked by insects; these compounds attract parasites and predators that kill the herbivores. Recent research is identifying more and more primary roles for these chemicals in plants as signals, antioxidants and other functions, so "secondary" may not be an accurate description in the future.

Consuming some secondary metabolites can have severe consequences. Alkaloids can block ion channels, inhibit enzymes, or interfere with neurotransmission, producing hallucinations , loss of coordination, convulsions, vomiting, and death. Some phenolics interfere with digestion, slow growth, block enzyme activity and cell division, or just taste awful.

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