Etheno-DNA adducts are generated from the metabolism of exogenous carcinogens and endogenous lipid peroxidation. We and others have previously reported that 1,N6-ethenodeoxyadenosine (εdA) and 3,N4-ethenodeoxycytidine (εdC) are present in human urine and can be utilized as biomarkers of oxidative stress. In this study, we report a new ultrasensitive UPLC-ESI-MS/MS method for the analysis of εdA and edC in human urine, capable of detecting 0.5 fmol εdA and 0.3 fmol εdC in 1.0 mL of human urine, respectively. For validation of the method, 20 human urine samples were analyzed, and the results revealed that the mean levels of εdA and εdC (SD) fmol/µmol creatinine are 5.82 ± 2.11 (range 3.0-9.5) for εdA and 791.4 ± 328.8 (range 116.7-1264.9) for εdC in occupational benzene-exposed workers and 2.10 ± 1.32 (range 0.6-4.7) for εdA and 161.8 ± 200.9 (range 1.8-557.5) for εdC in non-benzene-exposed workers, respectively. The ultrasensitive detection method is thus suitable for applications in human biomonitoring and molecular epidemiology studies.