There are more than 1,000 chemical compounds in coffee,^[1] and their molecular and physiological effects are areas of active research in food chemistry.

There are a large number of ways to organize coffee compounds. The major texts in the area variously sort by effects on flavor, physiology, pre- and post-roasting effects, growing and processing effects, botanical variety differences, country of origin differences, and many others. Interactions between chemical compounds also is a frequent area of taxonomy, as are the major organic chemistry categories (protein, carbohydrate, lipid, etc.) that are relevant to the field. In the field of aroma and flavor alone, Flament gives a list of 300 contributing chemicals in green beans, and over 850 after roasting. He lists 16 major categories to cover those compounds related to aroma and flavor.^[2]

The chemical complexity of coffee is emerging, especially due to observed physiological effects which cannot be related only to the presence of caffeine. Moreover, coffee contains an exceptionally substantial amount of antioxidants such as chlorogenic acids, hydroxycinnamic acids, caffeine and Maillard reaction products, such as melanoidins.^[3] Chemical groups, such as alkaloids and caffeoylquinic acids, are common insecticides; their effects on coffee quality and flavor have been investigated in most studies.^[4] Although health effects are certainly a valid taxonomy category, less than 30 of the over 1,000 compounds have been subjected to juried, health-related research (e.g. official potential carcinogen classification — see furans, for example), so health categorization has been avoided.

On the other hand, physiological effects are well documented in some (e.g. stimulant effects of caffeine), and those are listed where they are relevant and well-documented. Internet claims for individual chemicals, or compound synergies, such as preventing dental cavities (speculative but unproven effect of the alkaloid trigonelline with in vitro bacterial attachment research, but missing in vivo research on any health effects), preventing kidney stones, or negative effects, also have been avoided.

Chemicals found in coffee can be categorized in the following groups: