In situ hybridization (ISH) is a sensitive and specific technique for detecting nucleic acids in intact cells. Visualization of the target sequences by autoradiography or immunohistochemistry allows their precise subcellular localization and quantitation. The application of ISH techniques has contributed to the understanding of the complex replicative cycle of hepatitis B virus. More recently, hepatitis delta and C virus replication has also been studied by this technique. ISH-based assays have finally been used to follow the replication of cytomegalovirus within the transplanted liver. Although ISH is a powerful tool for the molecular biologist, its clinical significance in the diagnosis and prognosis of human hepatitis virus infections has yet to be fully evaluated.