Extreme temperature, drought and high salinity are common stress conditions that affect both plant growth and crop production. Molecular and genomic studies have shown that expression of many genes with various functions are induced by extreme temperature, drought and high salinity, and various signaling factors including transcription factors are involved in the stress responses. Gene chip, a microarray-based expression profiling method which profiles the expression of genes in the whole genome, combined with metabonomics and proteomics has allowed significant progress in the characterization of plant genes related to stress response and in the elucidation of the underlying anti-stress mechanisms. In this review, we highlight the advances of microarray analysis of stress condition related genes in plants. .