It has been suggested that lamivudine therapy can preselect for hepatitis B virus (HBV) variants associated with resistance to entecavir (ETV) treatment. The aim of this study was to determine the prevalence of HBV variants associated with ETV resistance (rtI169T, rtT184G, rtS202I, rtM250V) in naive patients before and during lamivudine therapy. This retrospective study includes 111 untreated patients with chronic HBV infection, who were later treated with lamivudine therapy for at least 18 months. Serum samples were obtained before and during treatment. Variants related with ETV drug resistance were analysed by sequencing the HBV reverse transcriptase. Prior to lamivudine treatment, three cases (2.7%) had substitutions in the HBV polymerase gene corresponding to variants associated with ETV resistance (rtS202S/I). None of these patients had lamivudine-resistant variants. During lamivudine treatment, substitutions associated with ETV resistance were detected in 10 (9%) nonresponding patients who had not presented these changes before treatment. In 2/10 cases, these changes were observed before detection of lamivudine-resistant substitutions. In 10 of 12 nonresponders, one of them with ETV-related variants prior to treatment, these variants persisted to the end of therapy. Detection of variants related to ETV drug resistance in untreated patients with chronic HBV infection indicates that these variants are present in a significant proportion of the HBV quasispecies. This fact, as well as the emergence of ETV-resistant variants during lamivudine treatment, should be kept in mind when selecting candidates for ETV therapy.