A sensitive and selective method for determination of the uracil content in human DNA was first developed on the basis of high-performance liquid chromatography-tandem mass spectrometry. Uracil was excised from DNA using uracil DNA glycosylase. The released uracil was derivatized with 4-bromomethyl-7-methoxycoumarin, thereby forming bis-N,N'-(4-methylene-7-methoxycoumaryl)-uracil (uracil-MMC). 15N2-Uracil was used as an internal standard. The analytes were separated on an Adsorbsphere XL ODS column. A SCIEX API III tandem mass spectrometer equipped with a turbo ion-spray interface was used as the detector. Multiple reaction monitoring using the parent --> product ion combinations of m/z 489 --> 232 and 491 --> 233 were used to detect uracil-MMC and the internal standard, respectively. The detection limit for this assay is <1.0 x 10(-10) mol/L uracil, and the linearity is from 1.0 x 10(-10) to 2.5 x 10(-6) mol/L. The method was used for determination of uracil in human DNA. Our data show that the uracil levels in human DNA isolated from peripheral white blood cells did not differ between subjects with folate deficiency and subjects with normal red cell folate levels.