Abstract: Diploid and haploid strains often exhibit different tolerances to variety of stresses, which facilitates the comparative studies to understand the mechanism of the tolerances to stresses. gene expression profiles of a diploid strain and two homologous haploid strains in the presence of ethanol at different concentrations were investigated by microarray and the data were validated with quantitative real time PCR. In all the three strains, upregulated genes in the presence of ethanol were involved in regulation of lipid synthesis and ribosomal biogenesis, while downregulated genes in the presence of ethanol were involved in synthesis of several amino acids, metabolism of biotin and folic acid. In addition, differentially expressed genes in different ploidy strains, which showed less responsive to ethanol, were involved in pheromone response or mating, energy, stress response, metal transport and cell wall. Furthermore, our data also revealed significant differences between transcriptome shift after ethanol acclimation and transcriptome response to short-term ethanol shock. Taken together, these results provide molecular insights into tolerance difference of haploid and diploid yeast strains and molecular information to further understand ethanol tolerance mechanism in yeast.CI - Copyright (c) 2010. Published by Elsevier B.V.