It is well established that DNA-associated proteins, as well as soluble free-radical scavengers, can significantly influence the amount of damage inflicted in DNA by ionising radiation. It is not known, however, to what degree there is variation between cell lines in the effectiveness of these cellular components to protect DNA. In this study we have examined the level of strand break induction in a human bladder carcinoma cell line, MGH-U1, and its radiosensitive mutant, U1-S40b, when soluble scavengers and DNA-associated proteins were progressively removed. DNA double-strand breaks were measured using pulsed-field gel electrophoresis when cells were irradiated after lysis in solutions containing various salt concentrations. The two cell lines showed only a small, non-significant difference in damage induced in intact cells but isolated nuclei and chromatin devoid of non-histone proteins showed significantly more damage in the U1-S40b cells. Once the histone H1 was removed again there was no difference between the cell lines in the damage induced. We conclude that the different components of the cellular defences against free radical attack can have different influences in different cells. It is not clear whether this has an influence on the cellular sensitivity to the killing effects of radiation but it does suggest that artificial manipulation of the different components of the system may not affect overall damage induction to the same degree in all cells.