The behavior of the chlorogenic acids (CGAs) and total polyphenols by the difference in roast degree of coffee beans was investigated. As samples, Coffea robusta and Coffea arabica from Brazil, six kinds of different roast degree beans and green beans, were used. HPLC/UV was used for the measurement of CGAs. LC separation was performed on a C18 column with a mixture of water–acetonitrile–acetic acid (1000:50:3) including 30 mg L−1 1-hydroxyethane-1,1-diphosphonic acid (HEDP), acetonitrile and methanol as the mobile phase, and calculated as 5-caffeoyl quinic acid (5-CQA). The Folin-Ciocalteu method was used for the measurement of total polyphenols, and calculated as 5-CQA. As the roasting increased, with both varieties, CGAs decreased, although most of the total polyphenols did not change. Therefore, a difference in roasting causes a change concerning the chemical structure of CGAs. However, the change substances had a hydroxyl group, which came from the structure of CGAs, and the possibility that had antioxidant ability was suggested.