Chlorogenic acid is a well-known antioxidant and has more isomers according to the difference in binding location and number of caffeic on quinic acid. In this study, we investigated and compared the profiles of antioxidant and DNA-protective activities of chlorogenic acid isomers including three caffeoylquinic acid isomers (3-O-caffeoylquinic acid, 3-CQA; 4-O-caffeoylquinic acid, 4-CQA; and 5-O- caffeoylquinic acid, 5-CQA) and three dicaffeoylquinic acid isomers (3,5-dicaffeoyl-quinic acid, ICAA; 3,4-dicaffeoylquinic acid, ICAB; and 4,5-dicaffeoyl-quinic acid, ICAC). The results showed that each of chlorogenic acid isomers studied exhibited antioxidant activities and DNA damage protective effects to various extents. On the whole, dicaffeoylquinic acids possessed better antioxidant activities, mostly because they have more hydroxyl groups than caffeoylquinic acids. Three caffeoylquinic acid isomers showed quite similar antioxidant activities, indicating that the position of esterification on the quinic moiety of caffeoylquinic acid had no effect on its antioxidant activities. Quite the contrary, a difference among dicaffeoylquinic acid isomers was observed, namely, ICAA and ICAB exhibited the same antioxidant activities, whereas ICAC had higher antioxidant activities than ICAA and ICAB in some assays, which implied that their antioxidant activities were probably influenced by the position of esterification on the quinic moiety. We speculated that this difference might be due to the fact that there may exist a steric hindrance effect in the ICAC. However, this assumption needs to be further confirmed.