Using an Affymetrix $GeneChip^{(R)}$ containing 8300 oligonucleotide probes, we measured transcript levels in transgenic Arabidopsis overexpressing the jasmonate carboxyl methyltransferase gene (AtJMT). When compared with wild-type plants, 5-week-old transgenics exhibited significant alterations (more than a two-fold increase or decrease) in the expression levels of 168 genes. Among them, 80 were up-regulated, including those involved in defense, oxidative stress-tolerance, and senescence. In contrast, the expression of 88 genes, including those that function in photosynthesis and cold/drought-stress responses, was significantly down-regulated. Thus, endogenous generation of methyl jasmonate through AtJMT-overexpression modified the transcript levels of genes previously identified as being jasmonate-responsive. This result confirms that MeJA formation is a key control point for jasmonate-responsive gene expression in plants.