Chlorogenic acids (CGA) are the main antioxidant compounds in the Western diet, due to their high concentrations in coffee associated with the high consumption of the beverage. Until about 10 years ago, like many other phenolic compounds, CGA were thought to be poorly absorbed in the human digestive system. Over the years, a large amount of information on the absorption and metabolism of these compounds have been unveiled, and today it is known that, on average, about one-third of the consumed CGA from coffee is absorbed in the human gastrointestinal tract, although a large inter-individual variation exists. Together with results from in vitro and animal studies, chlorogenic acids bioavailability supports, at least partly, the association between coffee consumption and lower incidence of various degenerative and non-degenerative diseases, in addition to higher longevity. Intestinal bacteria play an important role in the metabolization of the unabsorbed consumed CGA and probably also in the reabsorption of CGA excreted in digestive fluids.