DNA microarrays were used to investigate the transcriptional response of Saccharomyces cerevisiae genes under high temperature fermentation. Up to 35.73 % of yeast genes were up-regulated or down-regulated at least two-fold in their expression level at the late stage of fermentation. Nine genes involved in the pathways of glycolysis, ethanol generation and stress response were selected for study of their transcription profiles during high temperature fermentation processes by using quantitative real-time PCR assay. Our data indicated that the genes involved in trehalose biosynthesis and encoding heat shock proteins (HSPs) were significantly induced, while the genes involved in ethanol production were down-regulated during the 40°C fermentation. Specially, HSP26 displayed the highest transcription level of 166.19±15.82-fold at 6 h, indicating that this gene may play important roles at the onset of 40°C fermentation. Moreover, transcription levels of the nine genes were reduced significantly and returned to normal levels compared with controls after the samples were treated at 30°C for another 2 h. The results of this study suggest that these genes and their related pathways are involved in the response to high temperature; these findings will be helpful in improving the characteristics and fermentation capacity of industrial yeast strains by metabolic engineering.