Regulation of stress response in prokaryotes is mainly achieved at the transcriptional initiation level. Prokaryotes use alternative holoenzymes, consisting of the core polymerase associated with different sigma factors, which confer on it altered specificity of transcriptional initiation. Stress response being probably one of the most inevitable features of life, it would be interesting to find if eukaryotes also use a similar strategy at this level of regulation. Since the yeast Saccharomyces cerevisiae is a model system for studying many different phenomena in eukaryotes we review the transcriptional regulation of stress in this system. Based on published observations in the literature and our own studies, we have analysed the regulation of stress response, in the yeast S. cerevisiae. Two of the core subunits of the yeast RNA polymerase II, which show altered stoichiometry within the polymerase under different conditions appear to be involved specifically in regulating the stress response. In a very broad sense then, the altered subunit composition of the core polymerase or a different holoenzyme, appears to correlate with gene expression specific to stress response in S. cerevisiae and probably reflects the scenario in other eukaryotes.