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Bifunctional alkylating agent 1,3-Bis-(2-chloroethyl)-1-nitrosourea (BCNU) is a significant anticancer drug in the clinical treatment of human malignancies. A serious complication of treatment with BCNU is the increased risk of a secondary leukaemia in long-term survivors because not all alkylating agent interactions with DNA result in cell death. In the present work, high-performance liquid chromatography (HPLC) was combined with electrospray ionization tandem mass spectrometry (ESI-MS/MS) to develop a sensitive and selective method for the measurement of DNA adducts induced by BCNU. Double strand calf thymus DNA was treated with BCNU and digested enzymatically down to the nucleoside level. The hydrolysates were analyzed by HPLC separation followed by electrospray ionization tandem mass spectrometry. The main alkylated products, N7-(2-hydroxyethyl)deoxyguanosine (N7-HOEtdG), N7-(2-chloroethyl)deoxyguanosine (N7-ClEtdG) and 1-[N3-deoxycytidyl]-2-[N1-deoxyguanosyl]ethane (dG-dC) were qualitatively detected and quantitatively characterized by selected reaction monitoring (SRM) mode.