Bacillus subtilis exhibits a complex adaptive response to low levels of peroxides. We used global transcriptional profiling to monitor the magnitude and kinetics of changes in the mRNA population after exposure to either hydrogen peroxide (H(2)O(2)) or tert-butyl peroxide (t-buOOH). The peroxide stimulons could be largely accounted for by three regulons controlled by the PerR, sigma(B), and OhrR transcription factors. Three members of the PerR regulon (katA, mrgA, and zosA) were strongly induced by H(2)O(2) and weakly induced by t-buOOH. The remaining members of the PerR regulon were only modestly up-regulated by peroxide treatment. Overall, the magnitude of peroxide induction of PerR regulon genes corresponded well with the extent of derepression in a perR mutant strain. The sigma(B) regulon was activated by 58 micro M H(2)O(2) but not by 8 micro M H(2)O(2) and was strongly activated by either t-buOOH or, in a control experiment, tert-butyl alcohol. Apart from the sigma(B) regulon there was a single gene, ohrA, that was strongly and rapidly induced by t-buOOH exposure. This gene, controlled by the peroxide-sensing repressor OhrR, was not induced by any of the other conditions tested.