The mainstay of therapy for patients with chronic hepatitis B is inhibition of the replicative cycle of hepatitis B virus (HBV) in hepatocytes. Antiviral agents have different potencies. The measurement of HBV DNA in serum can monitor the potency of these therapeutic agents. Viral breakthrough may occur during therapy, which is defined as an abrupt increase in serum HBV DNA levels after a period of persistent suppression. The accuracy of HBV DNA detection depends on the sensitivity of assays. The third-generation quantitative assays have a lower limit of detection in ranges similar to those of quantitative PCR reaching 2 log10 copies/ml. The sensitive assays also give insight into the pathophysiology of chronic hepatitis B. Monotherapy usually suppresses the viral replication inadequately. It only brings about a reduction of serum HBV DNA levels from 8 to 4 log10 copies/ml. In other words, HBV is not completely eliminated. Viral breakthrough occurs with noncompliance to therapy and, also, when drug-resistant mutants emerge. Mutations in the YMDD motif of HBV polymerase lead to resistance to antivirals, such as lamivudine and famciclovir. In clinical practice, the diagnosis and management of viral breakthroughs are problematic and controversial. Due to advances in therapy, more potent agents are available such as adefovir dipivoxil that seldom induce viral breakthroughs for up to 134 weeks of therapy. Potent antiviral agents also lead to the decline of cccDNA in hepatocytes. Combination therapies may further improve efficacy and avoid viral breakthroughs.