Abstract Peroxidative damage to DNA initiated by methyl ethyl ketone peroxide, a potent initiator of lipid peroxidation, and protection against this damage by vitamin E were studied in rats. Groups of rats were fed a casein-based diet that contained 10% tocopherol-stripped cornn oil and either 0, 3, 5, or 10 IU of dl-α-tocopherol acetate/kg; the groups were named 0, 3, 5, or 10, respectively. DNA isolated from the brains of these rats was analyzed for template activity, bound tryptophan, and malondialdehyde-type DNA-protein and interstrand DNA crosslinks. The DNA of groups 5 and 10 had significantly higher template activity, less bound tryptophan, and fewer crosslinks than that of group 3 and 5, respectively. The DNA of group 3 had significantly fewer interstand DNA crosslinks than that of group 0, and the most significant differences were between groups 3 and 5. Loss of template activity correlated best with interstrand DNA crosslinks, and bound tryptophan correlated best with DNA-protein crosslinks. Electrophoresis of the RNA transcribed from the isolated DNA showed that a significantly higher percentage of longer RNA was made from the DNA of groups 5 and 10 than from that of group 0. The apparent molecular weight of the DNa of group 0 was less than that of group 10 and was more heterogeneous, which suggests fragmentation and/or crosslinking. The DNA from group 10 had maximum observed template activity; therefore, 10 IU of vitamin E/kg of diet appeared to be adequate to protect brain DNA against the damage measured in this study.