Toxicogenomics is a field of science that deals with the collection, interpretation, and storage of information about gene and protein activity within particular cell or tissue of an organism in response to toxic substances. Toxicogenomics meshes toxicology with genomics or molecular profiling, i.e. transcriptomics, proteomics and metabonomics.

This broad definition is supported by the United States Environmental Protection Agency stating that "the term "genomics" encompasses a broader scope of scientific inquiry and associated technologies than when genomics was initially considered. A genome is the sum total of all an individual organism's genes. Thus, genomics is the study of all the genes of a cell, or tissue, at the DNA (genotype), mRNA (transcriptome), or protein (proteome) levels. Genomics methodologies are expected to provide valuable insights for evaluating how environmental stressors affect cellular/tissue function and how changes in gene expression may relate to adverse effects. However, the relationships between changes in gene expression and adverse effects are unclear at this time and may likely be difficult to elucidate."

The nature and complexity of the data (in volume and variability) demands highly dvelopped processes for of automated handling and storage. The analysis usually involves a wide array of bioinformatics and statistics, regularly involving classification approaches.

In pharmaceutical Drug discovery and development toxicogenomics is used to study adverse, i.e. toxic, effects, of pharmaceutical drugs in defined model systems in order to draw conclusions on the toxic risk to patients or the environment. Both the EPA and the U.S. Food and Drug Administration currently preclude basing regulatory decision making on genomics data alone. However, they do encourage the voluntary submission of well-documented, quality genomics data. Both agencies are considering the use of submitted data on a case-by-case basis for assessment purposes (e.g., to help elucidate mechanism of action or contribute to a weight-of-evidence approach) or for populating relevant comparative databases by encouraging parallel submissions of genomics data and traditional toxicologic test results.

The National Academies Press: Communicating Toxicogenomics Information to Nonexperts: A Workshop Summary (2005)

Toxicogenomics: Principles and Applications; Ed.: H. K. Hamadeh and C. A. Afshari; Hoboken, NJ:Wiley-Liss, 2004. 361 pp. ISBN: 0-471-43417-5

EPA Interim Genomics Policy

Mattes et al. Environ Health Perspect. 2004 Mar;112(4):495-505

Ellinger-Ziegelbauer et al., Mutat Res. 2008 Jan 1:637(1-2):23-39

Environ Health Perspect. 2006 March: 114(3): 420-429