Interferons (IFN) are cytokines that have proinflammatory, antiviral and immunomodulatory effects, and play a central role during a host response to pathogens. The IFN family contains both type I and type II molecules. Whilst there are a number of class I IFNs, there is only one class II IFN. Recently both type I and type II IFN genes have been cloned in salmonid fish and recombinant proteins produced showing IFN activity. We have stimulated an Atlantic salmon cell line (SHK-1) with both type I and type II recombinant salmonid IFNs and analysed the transcriptional response by microarray analysis. Cells were exposed to recombinant IFNs for 6 or 24 h or left unexposed as controls. RNA was hybridised to an Atlantic salmon cDNA microarray (salmon 17K feature TRAITS/SGP array) in order to assess differential gene expression in response to IFN exposure. For IFN I and II, 47 and 72 genes were stimulated respectively, most genes were stimulated by a single interferon type, however, some were affected by both IFNs indicating co-regulation of the IFN response in fish. Real-time PCR analysis was employed to confirm the microarray results for selected differentially expressed genes in both a cell line and primary leukocyte cultures.