Hepatitis C virus (HCV) is a single-stranded RNA virus that replicates at a low level. Accordingly, the detection of HCV RNA requires molecular techniques such as reverse transcription polymerase chain reaction and branched chain DNA signal amplification assay. Although very sensitive, these assays do not allow specific localization of HCV within the liver. In situ detection of HCV genome and gene products is important to allow for the identification of cellular tropism, obtaining clues to the subcellular site of viral replication, and defining host-viral interactions. In situ hybridization, in situ reverse transcription polymerase chain reaction and immunohistochemistry have been applied for the localization of HCV genome and gene products. However, all these techniques were found to have their limitations and conflicting results have been reported based on all three techniques. This review will critically discuss the available data with an attempt to assist researchers to further understand the potential limitations and possible ways to solve these problems. The development of better protocols for the detection and localization of HCV will help to provide a better understanding of the pathobiology of HCV which, in turn, will assist in the design of better therapeutic strategies.