Atlantic salmon is one of the most important aquaculture fish species in the world. A cDNA library was constructed from splenic leukocytes of Atlantic salmon challenged with infectious pancreatic necrosis virus, and sequenced to collect genomic information and identify genes involved in immune defense response. Sequencing of 1360 clones yielded 1043 high quality ESTs (expressed sequence tags) and these ESTs were assembled into 823 unigenes. BLAST analysis revealed that 203 unigenes were novel genes that had no significant matches to any protein sequences in the public databases. The remaining 586 unigenes were closely matched to the known genes or sequences deposited in public databases and 34 unigenes matched to unknown genes. Among them, GO and KEGG analyses identified several functional categories involved in the innate immune response, with immune response and cytokine activity being predominant. These results provided a useful resource for gene discovery for further research of this species. (C) 2011 Elsevier B.V. All rights reserved.