Reactive oxygen intermediates (ROIs) are an evolutionarily ancient threat to all organisms. Both prokaryotic and higher eukaryotic cells are able to alter their genetic program in response to changes in the intracellular levels of ROIs. In bacteria and yeast, this response leads to the new synthesis of proteins that protect cells from the consequences of oxidative damage, such as DNA strand breaks, lipid peroxidation and oxidative damage of proteins. Intriguingly, higher organisms have also evolved cellular mechanisms to actively produce ROIs. There is increasing evidence that ROIs fulfil an important role as second messengers involved in signal transduction. We have proposed that ROIs have been conserved throughout evolution as universal pathogen messengers turning on genes with important functions in the immune response and cell proliferation. The higher eukaryotic transcription factors NF-kappa B and AP-1 will be described as proteins which are regulated by ROIs under a great variety of pathogenic conditions and initiate the new expression of genes with important roles in immune, inflammatory and other pathogen-related genetic responses.