Over the past decade, zebrafish are being increasingly used in assessing the effects of chemical compounds. Especially, the embryos and larvae, due to their microscopically small size and optical transparency, are compatible with multi-well microtiter plates for high throughput screening. Being transparent, they allow for non-invasive visualization of internal organs during early development. The organization of the genome, the genetic pathways controlling signal transduction and the developmental pattern appear to be significantly conserved between zebrafish and humans. Major organ systems including the nervous, cardiovascular, digestive and visual systems of zebrafish are also similar to their mammalian counterparts at the anatomical, physiological and molecular levels. Therefore, zebrafish assays are ideal for evaluating multiple organ toxicities simultaneously that contrast in vitro assays performed on cultured cells or tissue explants and organ slices. Although research on zebrafish as a model system began a few decades ago, later studies on zebrafish developmental biology and developmental genetics resulted in the characterization of a large number of genes involved in vertebrate development and biological pathways thus establishing zebrafish as a relevant human disease model for research. Recently, zebrafish have become an attractive vertebrate model for pharmaceutical and toxicological studies. We have outlined in this review some of the toxicological screens and tools that used zebrafish early life stages, and the efforts made to validate zebrafish assays against mammalian drug screens.