The purpose of this paper was to establish a method for the determination of modified bases, 5-methylcytosine and 8-hydroxyguanine, in DNA by GC/FID. The experimental conditions were explored systematically for the quantitative analysis of these two modified bases, and the components were identified by GC/MS. The results showed that the variant components in DNA treated with Fenton's reaction can be derivatized and separated successfully. The relative molar reactive factors of 5-methylcytosine and 8-hydroxyguanine were 3.0 and 1.3, respectively. The sensitivity for them were 5.50 x 10(9) mV.s/g and 7.59 x 10(10) mV.s/g, respectively, while their detectable limits were 36.4 pg/s and 15.8 pg/s, respectively. The coefficients of variation for gas chromatograph were less than 5%, for derivatization, less than 6%, and for the whole analysis process, less than 20%.