Chronic hepatitis C is a ubiquitous disease, affecting approximately 170 million globally. The hepatitis C virus (HCV) is spread by parenteral transmission of body fluids, primarily blood or blood products. The hepatitis C viral genome is a positive-sense, single-stranded RNA molecule approximately 9.4kb in length, which encodes a polyprotein of about 3100 amino acids. There are 6 main genotypes of HCV, with each further stratified by subtype. Hepatitis C virus exists as a heterogeneous mixture of closely related viruses called quasispecies. The continuous evolution of new variant glycoproteins is a major mechanism of viral evasion of the immune system. The quasispecies diversity collapses to oligoclonality or homogeneity prior to clearance. Substantial evidence indicates that HCV genotype is clinically important with respect to efficacy of anti-viral therapy. The dual drug regime currently used to treat HCV infection consists of pegylated-interferon (peg-IFN) and the guanosine nucleoside analog ribavirin. Mutations in the viral genome are likely to contribute in large measure to the emergence of “resistance” during interferon-based therapy. The HCV genome codes for 10 proteins. The structural proteins of core, E1, E2 and P7 are positioned immediately downstream of the 5;UTR. These proteins are cleaved from the polyprotein by host-encoded proteases. The remaining proteins are released from the polyprotein by a process of autocatalytic cleavage or by the protease activity of NS3. The RNA dependent RNA polymerase (NS5B) is position immediately downstream of the 3;UTR. The current cytokine based treatment modality is based on a shotgun approach of up regulation of cellular anti-viral pathways. The net effect of IFN signalling is the down regulation of protein translation. The cellular signalling pathways induced by IFN engagement of the cognate receptor are not specific for the elimination of HCV. HCV has evolved mechanisms that hinder IFN signalling and the induction of nuclease activity that would otherwise destroy the viral genome. The net benefit to the virus is that it potentiates the establishment of persistence. The activity of the host encoded proteases necessary for the cleavage of Core-P7, the proteolytic activity of NS3, the helicase activity of NS3 and the polymerase activity of NS5B are all potential targets for the development of adjunct options for the treatment of hepatitis C virus infections. The development of novel antivirals suitable for use against HCV has learnt a great deal from the research and development of drugs used to treat HIV disease. Like HIV, HCV has the propensity to produce greater than 1010 virions per day. Each genome will have a fitness potential to survive each unique selection pressure (endogenous and/or exogenous) and it is to be expected that again like HIV, HCV will have the potential to evolve drug resistant mutants. The goal of highly active antiretroviral therapy in HIV disease is viral suppression. However, it would appear that elimination, rather than suppression of viral replication, in HCV disease is achievable at least in a proportion of patients. The phenomenon of quasispecies is likely responsible for the ineffectiveness of isolate-specific vaccines and will challenge the development of pangenotype antiviral therapies. New strategies based on antisense and ribozyme technologies may hold future promise as therapeutic adjuncts in the treatment of HCV infection.