The existence of extrahepatic reservoirs of hepatitis C virus (HCV) replication remains highly controversial. We searched for the presence of HCV-RNA negative strand in various tissues from eight HCV-infected patients who died of acquired immunodeficiency syndrome (AIDS)-related complications. Negative-strand RNA was detected by a Tth-based reverse-transcriptase polymerase chain reaction (RT-PCR), which was optimized for sensitivity and strand specificity on synthetic RNA templates. This assay was capable of detecting about 10(2) genomic Eq molecules of the correct strand while unspecifically detecting >/=10(8) genomic Eq molecules of the incorrect strand. Negative-strand viral RNA was detected in all but one liver, in lymph nodes (5 cases), in pancreas (5 cases), in adrenal gland (2 cases), in thyroid (2 cases), in bone marrow (1 case), and in spleen (1 case). These data suggest a possible presence of HCV replication sites outside the liver, at least in AIDS patients. Whether these findings relate to various extrahepatic manifestations of HCV infection remains to be determined.