Toxicogenomics studies are built on standard toxicology studies, and one major goal of toxicogenomics is to detect relationships between changes in global gene expression and toxicological endpoints, including histopathology, clinical chemistry, and other toxicological parameters. In addition to interpret microarray data appropriately, it is desirable to perform comparative analyses with data obtained from well-characterized toxicants. Therefore, toxicogenomic databases containing high-quality global gene expression and traditional toxicological data are essential. The construction of a number of both public and private toxicogenomic databases has been initiated, including the Gene Expression Omnibus (GEO; National Center for Biotechnology Information, National Institutes of Health) database, the ArrayExpress (European Bioinformatics Institute) database, and various commercial databases developed by Gene Logic and Entelos. Considerable amounts of microarray data have been stored in these databases. In Japan, the Toxicogenomics Project (TGP), which is a collaboration consortium involving the National Institute of Health Sciences, the National Institute of Biomedical Innovation, and 15 pharmaceutical companies, has constructed a large-scale toxicogenomics database named Toxicogenomics project Genomics-Assisted Toxicity Evaluation (TG-GATEs) system. This database contains rat liver and kidney microarray toxicogenomic data for 150 compounds given to rats at three different dose levels. The data were collected at eight different time points following either single or repeated exposure. In vitro data sets contain information regarding the effects on rat and human hepatocytes resulting from exposure to the same compounds. The online version of this database, Open TG-GATEs, is now available for free public download. This project is currently in its second stage, known as the Toxicogenomics Informatics Project (TGP2). The goals of the TGP2 are as follows: establish genomic biomarkers for predicting the toxicity of drug candidates in the early stages of drug development, enhance ability to extrapolate accurately between experimental animals and humans, and apply toxicogenomic data as part of the regulatory decision-making process. These collaborative efforts will accelerate future advances in toxicogenomic research, and will contribute to the development of safer and more effective drugs.