A major progress has been made in the last decade in the understanding of molecular mechanisms involved in plant responses to stresses. This has been achieved in great part by application of a high-throughput genomics tools. Transcriptome analysis based on the DNA microarray technique has proved its effectiveness in studies of genome level responses to environmental changes and genetic manipulations. From the perspective of a decade, DNA microarrays serve as an invaluable tool for global gene expression analyses, unravelling new information about genes, pathways and their transcriptional regulation networks. In this review, we present applications of the DNA microarrays and a basic analysis of microarray data in relation to the transcriptional response of plants to ozone and drought stresses.