Many challenges exist for the study of HCV in the laboratory. Therapy using interferon (IFN) is expensive, not well tolerated and ineffective for many patients. HCV research has been hampered by the lack of a robust tissue culture system, but recent advances have made virus growth in culture possible. Cell culture systems using genetically engineered viruses have been reviewed extensively, but here we review recent advances made in the use of natural isolates and the molecular challenges that have been used to overcome the limitations in their growth. Six major genotypes have been identified for HCV that are further divided into numerous subtypes. Combination therapy utilizing IFN-α and ribavirin is the standard of care, but is successful in only one-half of patients. The reasons for IFN resistance may be viral- or host-related and may be due to multiple factors. Recently, telaprevir and boceprevir, together with IFN-α and ribavirin, have been added to the standard of care in patients infected with IFN-resistant genotypes. A major obstacle in the development of effective vaccines and improved therapeutics has been the lack of a reproducible and efficient tissue culture system for propagation of HCV. Many cell culture systems have used genetically-engineered viruses to gain growth in culture through the use of replicons, but recent advances using natural isolates may improve the outlook for progress in HCV research.