This work concentrates on the invitro metabolism of anthraquinone derivatives from rhubarb. Different metabolic reactions for anthraquinone derivatives were dependent on the substituent group in the skeleton. Monohydroxylation in the exocyclic methyl group was the major metabolic modification for emodin. Aloe-emodin containing a hydroxymethyl group was mainly metabolized through a methylation reaction. For rhein, both hydrogenation and methyl substitution on the benzene ring were the major metabolic reactions. Hydroxyl substitution on the benzene ring was the predominant metabolic reaction for chrysophanol. For physcion, demethylation of the exocyclic methoxy group was the most important metabolic reaction. Copyright © 2009 John Wiley & Sons, Ltd.