Baker's yeast (Saccharomyces cerevisiae) is one of the most essential ingredients in bakery products. During the commercial baking process, baker's yeast is subjected to baking-associated stresses such as high-sugar concentrations, air-drying and freezing. These stresses significantly influence cell growth and fermentation. To avoid lethal damage, yeast cells need to adapt to the harsh environments. In order to clarify which genes are important for adaptation to stresses, a functional genomics analysis was carried out under stress conditions that simulated those occurring during the fermentation of dough and the production of dried yeast. Gene expression profiles indicated that many genes are involved in stress tolerance in yeast. In particular, it was suggested that the folding of intracellular proteins and the removal of denatured proteins play important roles in yeast cells under stress conditions. Additionally, it was suggested that the increased expression of genes involved in energy production is important for adaptation to stresses. We expect that these gene expression profiles accelerate improvements in the breeding of baker's yeast that has higher tolerance to stresses.