C urrent therapy of chronic hepatitis C virus (HCV) infection is based on type I interferon (IFN) preparations. 1 The IFNs comprise a class of related cytokines that induce antiviral and immunomodulatory actions of their target cells. 2,3 The type I IFNs include multiple IFN-␣ species and a single IFN- species ( Fig. 1), and IFN-␥ is the single type II IFN. 3 The commercial IFN preparations that are largely used for HCV therapy consist of IFN-␣2a or IFN-␣2b subtypes. 4 The type I IFNs bind to a common receptor that is expressed on the surface of target cells. Receptor engagement leads to the activation of the Jak-STAT signaling pathway through the actions of the Jak1 and Tyk2 protein kinases, which catalyze phosphorylation events leading to the activation and heterodimerization of the signal transducer and activator of transcription (STAT) proteins STAT1 and STAT2. 2 STAT3 has also been shown to respond to type I IFN receptor signaling and is proposed to link IFN signaling events with cell growth regulation and the phosphatidylinositol 3-kinase pathway. 5,6 The STAT1/2 heterocomplex translocates to the cell nucleus, where it associates with p48/IRF-9 to form interferonstimulated gene factor 3 (ISGF3). 2 ISGF3 binds to the IFN-stimulated response element (ISRE) of cellular genes, known as IFN-stimulated genes (ISGs), leading to their induced expression and synthesis of the ISG products. Sequence motifs within the ISRE also serve as target sites for interferon regulatory factors (IRFs), whose actions and ISRE-binding properties contribute to define the overall spectrum and duration of ISG expression. 2,3 It is the biochemical actions of the ISG products that impart the primary therapeutic actions of IFN against HCV infection. However, IFN therapy continues to be problematic, because even under the best conditions, contemporary treatment protocols show limited efficacy such that only about one half of all treated patients exhibit sustained viral clearance. 1,4 The reasons for this limited efficacy are unclear, but are likely to involve both viral and host factors that ultimately affect the level and extent of ISG expression and function induced during the course of IFN therapy. [7][8][9][10] Results from microarray expression studies indicate that the human genome encodes hundreds, if not thousands of functionally diverse ISGs, some of which are known to direct antiviral actions. 11 However, the complete spectrum of ISGs has not been defined nor have the ISGs that impart control of HCV replication been identified. The refinement and further improvement of IFN therapy for chronic HCV infection will no doubt come from a better understanding of how IFN affects the infected hepatocyte and other target cells. This requires defining the spectrum and kinetics of ISG expression under in vivo conditions of IFN therapy and categorizing ISG expression patterns within patients who respond to therapy and in those patients who fail IFN therapy. In vivo studies that couple analyses of viral decay kinetics with microarray profili...