Hepatitis C virus (HCV) core proteins from two different isolates (HCV-1 and HCV-RH) were expressed in Spotioptera Jrugiperda (Sf9) insect cells. The RH core consisted of two major species of proteins (21 kDa and 19 kDa). On the other hand, the HCV-1 core was approximately 16 kDa in a SDS-PAGE gel. Both core proteins were phosphorylated in vivo on serine residues. Furthermore, the RH core but not HCV-1 core formed dimers, indicating that the protein conformation of the core in these two isolates is dfferent from one another. Immunofluorescence studies showed that the RH core was present in the cytoplasm, whereas the HCV-1 core was localized predominantly to the nucleus in recombinant baculovirus-infected insect cells. Since the major difference between the two isolates is the codon 9 of the core protein, a single amino acid substitution appears to play a major role in the protein conformation and these properties may reflect the different biological functions of core proteins in HCV-infected cells.