Chlorogenic acid (3-O-caffeoylquinic acid, CA) is the active component in several botanical beverage, vegetables, fruits, and herbal drugs. The effect of water boiling on the bioactivity of CA was studied. CA could be isomerized to 4-O-caffeoylquinic acid (4-O-CA) and 5-O-caffeoylquinic acid (5-O-CA) in decoctive extraction, and each of the isomers occupied about one-third of the total caffeoylquinic acids. A novel method, using water elution of microsphere resin, was used to purify CA and its 2 isomers. The yield of CA, 4-O-CA, and 5-O-CA was 82%, %, and 50%, with the purity of 98%, 97%, and 99%, respectively. The DPPH radical scavenging assay showed that 4-O-CA, 5-O-CA, and CA exhibited similar activity. However, there was no significant difference between 4-O-CA and 5-O-CA when used against CCl₄-induced toxicity in hepG2 cells. Our studies show that isomerization is the main transformation of CA in boiling, and the decoction could not decrease the anti-oxidant activity of CA.