To obtain global gene expression profiles of Arabidopsis thaliana by acid stress, seedlings were subjected to low pH stress. Using Affymetrix AH1 chips covering 24,000 genes, we analyzed gene expression patterns. Fifty-four genes were up-regulated, and 38 were down-regulated more than 3-fold after 2 h of acid stress (pH 3.0). Several defense and abiotic stress-related genes were recognized among the up-regulated genes and peroxidase and extensin genes were identified among the downregulated genes. After 12 h treatment, relatively fewer genes showed changed expression, indicating that plants seem to adjust themselves to this abiotic stress. Most of the up-regulated genes are already known to be involved in abiotic stress responses and pathogen attacks, especially wounding. However, down-regulated genes for the members of extensins and peroxidases are specific to the acid treatment. These results suggest that acid treatment turns on genes involved in stress responses, especially in wounding and turns off genes very specific for the acid stress.