The increased concern for the security of the oil supply and the negative impact of fossil fuels on the environment, particularly greenhouse gas emissions, has put pressure on society to find renewable fuel alternatives. Compared to the traditional biofuel, ethanol, higher alcohols offer advantage as gasoline substitutes because of their higher energy density and lower hygroscopicity. For this reason, microbial fermentation is known as potential producers for sustainable energy carriers. In this study, bacterial responses including cellular and molecular toxicity were studied in three different microorganisms, such as Escherichia coli, Clostridium acetobutylicum, and Saccharomyces cerevisiae. In this study, it was analyzed specific stress responses caused by ethanol and buthanol using four different stress responsive genes, i.e. fabA, grpE, katG and recA. The expression levels of these genes were quantified by semi-quantitative reverse transcription-PCR. It was found that four genes have shown different responsive patterns when E. coli cultures were under stressful conditions caused by ethanol and buthanol, respectively. Therefore, in this study, the stress responsive effects caused by these alcohols and the extent of each stress response can be analyzed using the expression levels and patterns of different stress responsive genes.