The more recently introduced molecular tests that detect and quantify viral genomes complement the information obtained immunologically and, due to rapid turnaround times and the availability of user-friendly commercial kits, have acquired a key position in both the diagnosis and the follow-up of viral hepatitis. Direct detection of the infectious agent has an ancillary role in the laboratory diagnosis of hepatitis A due to the reliability and ease of anti-hepatitis A virus (HAV) immunoglobulin M (IgM) testing. Viral RNA is tested for mainly by reverse transcriptase PCR (RT-PCR). Certainly more important for laboratory diagnosis and disease management, however, are the so-called hepatitis B e antigen (HBeAg)-minus core or precore mutants of the virus, which are unable to express HBeAg due to a stop codon in the C gene, and the drug-resistant variants that are commonly found in patients undergoing therapy. Qualitative nucleic acid-based tests are most useful in assessing the safety of blood donations but prove useful also when a suspicion of active infection based on serological grounds needs to be confirmed. In this case, it is advisable to retest negative patients several times at intervals of several weeks in order to identify the ones who might have intermittent viremia, as is frequently observed in the course of spontaneous resolution or antiviral therapy.