Topiramate (TPM) is a novel neurotherapeutic agent approved for the treatment of epilepsy and for migraine prophylaxis. It has been observed that in obese-associated, type 2 diabetic rodent models, TPM treatment reduced the body weight gain, improved insulin sensitivity, and enhanced glucose-regulated insulin release. A long-term treatment with TPM thus ameliorated obesity and diabetic syndromes in female Zucker diabetic fatty rats and db/db mice. The molecular mechanisms of TPM antiobesity and antidiabetic effects remain unknown. We have applied DNA microarray technology to explore genes that might be involved in the mechanisms by which TPM improves insulin sensitivity and blood glucose handling, as well as body weight control. In female Zucker diabetic fatty rats, 7-day TPM treatment significantly reduced the plasma levels of glucose and triglyceride in a dose-dependent manner. The DNA microarray data revealed that TPM treatment altered messenger RNA profiles in liver, hypothalamus, white adipose tissue, and skeletal muscle. The most marked effect of TPM on gene expression occurred in liver with those genes related with metabolic enzymes and signaling regulatory proteins involved in energy metabolism. TPM treatment decreased messenger RNA amounts for sterol regulatory element binding protein-1c, stearoyl-coenzyme A (CoA) desaturase-1, choline kinase, and fatty acid CoA ligase, long chain 4. TPM also up-regulated 3 cholesterol synthesis genes. In addition, the short-term effect of TPM on gene expression was examined at 16 hours after a single administration. TPM markedly reduced hepatic expression of genes related with fatty acid synthesis, eg, stearoyl-CoA desaturase and acetyl-CoA carboxylase. TPM also changed genes related with fatty acid beta-oxidation, increased 3-2-trans-enoyl-CoA isomerase and mitochondrial acyl-CoA thioesterase, and decreased fatty acid CoA ligase (long chain 2 and long chain 5). These gene expression changes were independent of food intake as shown by pair feeding. Our results suggest that TPM regulates hepatic expression of genes involved in lipid metabolism, which could be part of the mechanisms by which TPM reduces plasma triglyceride levels in obese diabetic rodents.