A sensitive and specific HPLC-MS-MS method was developed for the determination of endogenous uracil (Ura) and its metabolite dihydrouracil (UH2) in human plasma and urine samples. Plasma samples were extracted with ethyl acetate-isopropanol (85:15, v/v) following added ammonium sulfate, and then separated on a Discovery Amide C16 column with 3% methanol solution as the mobile phase; urine samples were just centrifuged at 2500 g for detection. Quantitation was carried out by LC-MS-MS in the multiple reaction monitoring (MRM) mode. The limits of quantitation of the method for Ura and UH2 were 0.5 and 5 ng ml(-1) (for plasma), and 50 and 100 ng ml(-1) (for urine), respectively. This method can be useful to evaluate the activity of dihydropyrimidine dehydrogenase (DPD), a rate-limiting enzyme of the chemotherapy drug fluoropyrimidine, which will be helpful in investigating subject variation of DPD and adjusting clinical dosage in pyrimidine chemotherapy.