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A rapid, simple and sensitive ultra high-performance liquid chromatography (UHPLC-MS/MS) method was established for determining the absorption amount of emodin in the five digestive segments of rat. Plasma samples were pre-purified by solid-phase extraction (SPE) with Oasis MAX cartridge. Separation of emodin and 1,8-dihydroxyanthraquinone (internal standard) was performed on an Acquity BEH UHPLC C-18 column (100 mm x 2.1 mm, 1.7 mu m) with gradient elution of methanol and 0.1% formic acid aqueous solution. The LC/MS system was operated under multiple reaction monitoring mode using electrospray ionization (ESI) in negative ion mode. The results showed that this established method was valid and sensitive for ernodin within 0.04-16.4 mu g/mL, with low limits of detection and quantification of 0.6 ng/mL and 2.4 ng/mL, respectively and upper limit of quantification of 220.0 ng/mL. The intra- and interday variations were below 4.9% of RSD. The extraction recoveries were 98.9-106.1% with RSD of 1.9-3.2%. The plasma concentration-time relationship showed that the absorption of emodin in stomach was faster than in intestine segments. The sequence of absorption amount was: ileum > jejunum > colon approximate to duodenum > stomach. Most of emodin was absorbed in ileum, and the absorption amount was increased with prolonged retention of drug form in intestine, especially in ileum and jejunum. The developed UHPLC-ESI-MS/MS method was appropriate for determining the in vivo absorption of emodin in other herbal medicines or preparations containing this compound.