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Technological advances in the biological sciences have led to a growing realization of the inherent complexity of the toxic actions of man-made chemicals and industrial compounds. An organism's response to toxic exposure is often a complex summation of the individual responses of various different cell types, tissues, and organs within an individual. Furthermore, within a population, various factors including gender, age, fitness, exposure history, genetic variation, and developmental stage significantly affect how each individual will react following exposure. Because of this complexity, characterizing the responses of organisms to environmental toxin exposure is an area of research well suited to the utilization of the gene-expression profiling capability of DNA microarrays. Microarrays are capable of screening large numbers of genes for response to environmental exposure, with the resulting genesets comprising de facto biomarkers for such exposures. In many cases, the genesets described contain response transcripts anticipated from known mechanistic pathways, but in other cases, equally indicative biomarkers may be found that are unexpected. We investigated the response of zebrafish embryos exposed in vitro to the environmental contaminant 4-nonylphenol (4NP). Nonylphenol is one of several alkylphenol ethoxylate compounds widely used in agricultural and industrial processes that have become ubiquitous environmental contaminants. By combining data from differing levels of exposure, we have identified a group of genes that appear indicative of embryo exposure to 4NP at concentrations ranging from high near-lethal levels to lower, more environmentally relevant levels. These biomarker sets can be further expanded and adapted for use in environmental monitoring as well as in mechanistic studies of complex toxicological mechanisms during both early and adult developmental stages.