Phenolic compounds are secondary metabolites generally involved in plant adaptation to environmental stress conditions. Chlorogenic acids (CGA) and related compounds are the main components of the phenolic fraction of green coffee beans, reaching levels up to 14 % (dry matter basis). These compounds have a number of beneficial health properties related to their potent antioxidant activity as well as hepatoprotective, hypoglycemic and antiviral activities. The main groups of CGA found in green coffee beans include caffeoylquinic acids, dicaffeoylquinic acids, feruloylquinic acids, p-coumaroylquinic acids and mixed diesters of caffeic and ferulic acids with quinic acid, each group with at least three isomers. During coffee processing, CGA may be isomerized, hydrolyzed or degraded into low molecular weight compounds. The high temperatures of roasting also produce transformation of part of CGA into quinolactones and, along with other compounds, melanoidins. This review focuses on the chemical characteristics, biosynthesis, and distribution of CGA and related compounds in coffee. The influence of genetic, physiological and environmental factors as well as processing on the chemical composition of coffee beans is discussed. The impact of CGA composition of green coffee on cup quality is also approached. Despite the existence of substantial published information on the total levels of CGA in coffee, more research is needed on the composition of minor phenolic compounds and specific CGA isomers (and related substances) in green and roasted coffee beans, as well as their impact on coffee quality.