In the present work, we examined the formation and repair of DNA base damages induced by gamma-irradiation in different fractions of rat hepatic chromatin. Animals were exposed to radiation with the dose of 10 Gy. Nuclear matrix DNA and whole chromatin were isolated from the liver of rats killed before and in different time after irradiation. In those samples the pyrimidine-derived and the purine-derived modified DNA bases were identified and quantitated by gas chromatography/isotope-dilution mass spectrometry with selected-ion monitoring. We found elevated levels of modified DNA bases over control values after whole body irradiation in both matrix DNA and bulk chromatin samples. Our results suggest that modified bases are preferentially removed from matrix DNA then bulk chromatin.