The treatment of HBV infected patients with analogues of nucleos(t)ides, including lamivudine and adefovir dipivoxil, has significantly increased the rate of anti-HBe seroconversion and therefore reduced the impact of chronic hepatitis B (CHB) on liver disease. Altogether, these antivirals have offered novel options for the treatment of patients who did not respond to previous therapy with interferon alpha, the only available treatment against CHB until 1998. However, therapies using analogues of nucleos(t)ides have been confronted with viral resistances which are often associated to with worsening of liver disease. Drug resistance is conferred by the appearance of one or several mutations within the HBV polymerase gene. These mutations confer to the mutant viral population a phenotypic advantage over the wild-type pretherapeutic viral quasispecies, as they induce a reduction of drug susceptibility of mutant strains in vivo. This reduction of drug susceptibility can be as well measured in vitro, i.e in cell culture, using phenotypic assays. The detection of these mutations has become of crucial importance to better adapt clinical option to the virological status of the patient. Genotypic and more recently phenotypic assays have been developed and both assays can be used for drug resistance testing. Genotypic assay gives information about already characterized mutations associated with viral resistance, while phenotypic testing measures the overall drug susceptibility of patient-derived viral strains in cell culture. These assays are described and their potential use in the clinical setting is discussed.