All organisms respond to environmental, chemical and physiological stresses by enhanced synthesis of an evolutionarily conserved family of proteins known as heat shock proteins (HSPs) or stress proteins. Certain HSPs are also expressed constitutively during cell growth and development, and they function as molecular chaperones. The transcriptional regulation of hsp genes is mediated by the heat shock transcription factor (HSF). The stress response has been studied mostly in mammalian cell lines or organisms normally maintained under constant laboratory conditions. There is much less information on the regulation of the stress response of animals, such as fish, that have to tolerate large fluctuations in environmental and internal conditions. To characterize the regulation of the heat shock response in fish, we have cloned the first heat shock transcription factor from fish, zebrafish Danio rerio. Phylogenetic analysis confirms that the isolated zebrafish HSF belongs to the HSF1 family and is therefore designated zHSF1. Analysis by reverse transcriptase polymerase chain reaction (RT-PCR) shows the presence of two zHSF1 mRNA forms that are expressed in a tissue-specific fashion upon exposure to heat stress. Both forms are expressed in gonads under all conditions; in liver and to a lesser extent in the gills, the longer splice form of zHSF1 disappears upon heat shock. We present evidence for a unique tissue-specific regulation of HSF1 upon exposure to elevated temperature.