Neochlorogenic acid (3-CQA) and cryptochlorogenic acid (4-CQA), isolated from prune (Prunus domestica L.), were identified by NMR and MS analyses. In addition, the quantity of chlorogenic acid isomers in prune were measured by HPLC. These isomers, 3-CQA, 4-CQA, and chlorogenic acid (5-CQA), were contained in the ratio 78.7:18. 4:3.9, respectively. 4-CQA was identified and quantified in prune for the first time, and relatively high amounts of this isomer were characteristic. Antioxidative activities of the chlorogenic acid isomers, such as scavenging activity on superoxide anion radicals and inhibitory effect against oxidation of methyl linoleate, were also evaluated. Each isomer showed antioxidative activities which were almost the same.