Hydroxyl radical-mediated modifications of nucleobases are among the main deleterious processes induced in DNA by ionizing radiation. Determination of the underlying mechanisms in both isolated and cellular DNA requires the development of accurate assays for the detection of modified bases. High-performance liquid chromatography associated with electrochemical detection (HPLC-EC) and gas chromatography coupled to mass spectrometry (GC-MS) are the two main methods used for this purpose. In the present work, HPLC-EC was applied to the measurement of 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-oxodGuo) following enzymatic digestion of DNA. Evidence was provided for the quantitative aspect of the latter step. Moreover, a GC-MS assay was designed for the detection of 2,6-diamino-4-hydroxy-5-formamidopyrimidine (FapyGua). It was first shown that the widely used hot formic acid hydrolysis of DNA induced a complete decomposition of the lesion. A similar observation was also made for 4,6-diamino-5-formamidopyrimidine (FapyAde). A milder DNA hydrolyzing agent, HF in pyridine, was substituted to HCOOH for the quantitative release of FapyGua from DNA. The radiation-induced formation of 8-oxodGuo and FapyGua in aqueous solution of DNA was compared. Insights in the mechanistic aspects were inferred from the results of γ-irradiation studies carried out under different gas saturating conditions. It was clearly shown that the formation of both lesions is mediated by HO(O). In addition, the presence of oxygen favors the formation of 8-oxodGuo at the expense of FapyGua.