We have analyzed the molecular bases of the persistence of hepatitis B virus (HBV) DNA in serum and peripheral blood mononuclear cells (PBMC) in the absence of detectable hepatitis B surface antigen (HBsAg) in hemodialysis patients and dialysis-unit staff members who had suffered acute hepatitis B that resolved previously. HBV DNA was found in both compartments by polymerase chain reaction (PCR) using primers of the pre-S/S region. Viral DNA was transcriptionally active in PBMC, because the covalently closed circular (ccc) HBV DNA, the template for the viral RNA transcription, was detected in 47% of the samples. Furthermore, all PBMC had HBV RNA. HBsAg-negative cases had statistically lower levels of HBV DNA in serum and PBMC than a control group of chronic HBsAg carriers. We have also studied the presence of immune complexes and the existence of mutations in the pre-S/S gene to explain the lack of detection of HBsAg in these cases. No serum HBsAg/hepatitis B surface antigen antibody (anti-HBs) immune complexes or mutations in the “a” determinant of the S gene were found. However, we have observed that all HBsAg-negative cases were infected by a mixture of the wild-type virus and a deletion mutant in the pre-S1 region. This deletion (amino acids 58-118) affects the S gene promoter, and previous in vitro studies have shown that it produces a reduction of the HBsAg synthesis. In conclusion, this work shows that the lack of detection of HBsAg in the presence of low viral levels of replication may be caused by the existence of viral genomes harboring deletions in the pre-S1 region that affect the S promoter.