The development of DNA microarrays has provided a powerful new tool for investigating the gene expression changes that underlie response to toxicant exposure. The technology promised great improvements in understanding modes of action, the possibility of rapid toxicity screening of novel chemicals, and the potential for developing new methods of environmental monitoring. However, the technology has yet to truly deliver on these initial promises. Largely this can be attributed to the use of suboptimal experimental and statistical approaches. The aim of this study was to develop the application of gene expression profiling using microarrays to toxicity testing in the zebrafish embryo.