Examination of a naturally infected human liver and experimentally infected chimpanzee and woodchuck livers by in situ hybridization showed that hepatitis delta virus (HDV) RNA was restricted to hepatocytes. Genomic RNA was 20-30 times more abundant than antigenomic RNA and was predominantly single-stranded while antigenomic RNA was predominantly double-stranded. In acute delta hepatitis, viral RNA was a more reliable marker of virus infection in single cells than hepatitis delta antigen (HDAg) while in chronic hepatitis both markers were usually present in the same cell. In all cases, viral antigen and RNA were localized predominantly to the nuclei of infected cells. Thus, replication of HDV RNA is closely associated with HDAg expression at the cellular and intracellular level and it is likely that this new class of defective animal RNA viruses replicates in the nucleus of the infected cells.