Liver and serum samples from 67 children with hepatitis B chronic infection, whether or not treated with recombinant interferon, were analyzed for the presence of hepatitis B virus DNA. After follow-up, 44/67 (66%) still had serum and liver viral DNA; 23/67 (34%) were negative for serum hepatitis B virus DNA. Of the 23 children in the latter group, liver biopsy was available in 21 and viral DNA was not detected by Southernblot in 20. In the remaining patient, viral DNA was in an episomal nonreplicative form. Polymerase chain reaction was performed in the 21 serum samples negative for viral DNA by conventional techniques and in the 21 liver samples (20 negative for hepatitis B virus DNA and 1 with episomal nonreplicative form). All liver samples resulted i n a positive reaction t o viral DNA by this technique. Serum viral DNA by polymerase chain reaction was detected in 15/21 (71%) of these patients. The mean of alanine aminotransferase values was similar in patients with or without hepatitis B virus DNA in serum by polymerase chain reaction. In summary, in the majority of the patients who respond to the therapy, there is a persistence of viral replication detected by polymerase chain reaction. This fact explains the persistence of serum HBsAg in these patients. However, more studies are necessary to determine the meaning of the presence of hepatitis B virus DNA that is only detectable by polymerase chain reaction. © 1992 Wiley-Liss, Inc.