Type I (α, β) and type II (γ) interferons (IFN) possess pleiotropic functions, including antiviral, antiproliferative and immunomodulatory activities, which are likely mediated by the induction of unique subsets of IFN-stimulated genes (ISG) that are differentially regulated by IFN subtypes and in different cell types. Oligonucleotide arrays (Affymetrix) were used to investigate differential gene expression in the human fibrosarcoma cell line, HT1080, or primary mouse embryonic fibroblasts in response to IFNs or virus infection. In all samples, the detection of known IFN-regulated genes helped to validate the experimental design and conditions. Combined analysis of these data sets, each with several hundreds of differentially expressed genes, has led to the idenfication of groups of IFN-regulated genes with similar functions, previously unknown IFN-regulated pathways and potential to crosstalk with other signalling pathways. For example, ISGs with similar functions included apoptosis regulators, chemokines, genes involved with antigen processing and presentation, GTPases, heat shock proteins and members of the ubiquitin system. Signalling molecules identified as potentially novel ISGs included known kinases, phosphatases and signalling adapter molecules. The functional significance of each gene relating to IFN functions requires further study on an individual basis, but the continuous refinement of a global view for IFN-regulated pathways may identify additional yet unknown areas of IFN action and enable better design of therapeutic strategies based on IFN-regulated mechanisms.