Molecular methods are a well-established part of routine diagnostic work-up in patients infected with hepatitis B virus (HBV) and hepatitis C virus (HCV). Confirmation of active viral replication in infected patients is based on detection and/or quantification of viral genome in serum by molecular assays. Diagnostic algorithm for hepatitis C includes detection and/or quantification of HCV RNA in serum of infected patients and HCV genotyping. Diagnostic work-up in patients with hepatitis B includes quantification of HBV DNA in serum, HBV genotyping, and determination of resistance to nucleoside and nucleotide analogues. Real-time polymerase chain reaction (PCR) is the standard recommended molecular method for quantification of HCV RNA and HBV DNA in clinical samples. Due to superior sensitivity, real-time PCR assays can provide both qualitative detection of viral genome and quantification. Molecular diagnosis of HCV and HBV infections in clinical laboratories should be limited to certified standardized assays.