Interferon regulatory factors (IRFs) are a large family of transcription factors involved in regulating the transcriptional response of vertebrates to interferons and viral infection. In this report we describe the cloning and genomic organization of an IRF gene from the pufferfish (Fugu rubripes). The fugu IRF gene spans 2.7 kb from the transcription start site to the polyadenylation signal. It consists of 10 exons and 9 introns and encodes a protein of 296 amino acids. The overall amino acid sequence of fugu IRF displays 55% identity to flounder IRF and approximately 44% identity to avian and mammalian IRF-1 and IRF-2. On the basis of the genomic structure and the absence of a transcriptional repression domain, we conclude that the fugu IRF is a member of the IRF-1 family. The fugu IRF gene is expressed in a wide range of tissues. While a single transcript of 1.4 kb was detected in most tissues, several larger transcripts generated using alternative polyadenylation signals were found in the gills.