Interferon responses are balanced between protection against pathogens and other disease agents versus toxicity and development of chronic diseases. Optimal outcomes are achieved by regulating the nature, strength and duration of Interferon (IFN) production, IFN-receptor interaction and signalling pathways modulated in a manner appropriate for particular target cells. Modification of cell behaviour is mediated by regulation of positive and negative signalling pathways and by proteins encoded by selected groups of IFN-regulated genes. Understanding how these pathways are regulated and how to measure them by biomarkers or gene signatures will enable us to better understand the role of IFN pathways in the pathogenesis of infectious and inflammatory diseases and cancer. This will lead to improved patient stratification and disease treatment.