We developed a new method for the simultaneous quantitative determination of 8-oxo-7,8-hydro-2'-deoxyguanosine (8-oxodGuo), 8-oxo-7,8-dihydroguanine (8-oxoGua), 8-oxo-7,8-dihydroguanosine (8-oxoGuo), and the corresponding non-oxidized forms, 2'-deoxyguanosine (dGuo), guanine (Gua) and guanosine (Guo), in human urine samples by liquid chromatography-tandem mass spectrometry. Differences in the ionization of analytes in different urine batches with variable matrix effects were effectively compensated for by internal standardization with stable isotope-labelled analytes. The method was sensitive enough to allow the determination of background levels of these biomarkers and was applied to characterize the inter- and intraindividual variability of biomarkers in the diurnal profile of concentrations in 24 healthy volunteers. When normalized for creatinine, none of the biomarkers was affected by sampling time, thus ruling out any circadian rhythm for nucleic acid oxidation in urine.