The reaction of styrene oxide with DNA components was studied using separation by capillary zone electrophoresis (CZE) and detection by negative-ion electrospray mass spectrometry (MS). The CZE-MS interface was built for a sector field mass spectrometer. The reaction of styrene oxide with mononucleotides (dGMP, dAMP) was used to optimize the relevant separation parameters and to gather the first information about the behaviour of the possible products. With these mixtures, sample stacking procedures were developed and the scope of collision-induced dissociations were studied. From the fragments recorded, information about the reaction sites in the nucleotides was obtained. Further, the reaction with intact calf thymus DNA was investigated. The DNA was digested into oligonucleotides using the previously described approach with Benzonase, an unspecific nuclease, and alkaline phosphatase. Styrene oxide mono-adducts in dinucleotides, trinucleotides and tetranucleotides were detected, whereas pentanucleotides exhibit mono- and discernible amounts of di-adducts. The hexanucleotides were generally modified twice. The alkylated species moved faster than the unmodified oligomers.