Anthraquinones are a major group of polyphenols in the rhizome of Rheum palmatum L. (RP). This study investigated the metabolism and pharmacokinetics of anthraqinones in RP decoction in rats. The concentrations of four anthraquinones including aloe-emodin, rhein, emodin, chrysophanol, and their glycosides in the decoction were quantitated by HPLC before and after acid hydrolysis with the results indicating that the anthraquinones mainly existed as the glycoside form except for rhein. Rats were orally administered RP decoction and blood samples were assayed by HPLC before and after treatments with sulfatase and beta-glucuronidase. It was found that the glucuronides of aloe-emodin, rhein, emodin and chrysophanol were predominant in the blood, whereas their aglycones were not detected except for rhein. In conclusion, the anthraquinones were subject to a rapid and extensive conjugation metabolism in rats and the serum metabolites of RP exhibited a potential free radical scavenging effect on AAPH-induced hemolysis at pharmacologically relevant concentrations.