All human hepatitis B viruses characterized so far express three envelope proteins, pre-S1, pre-S2, and HBs, which are believed to function as binding proteins for the cellular receptor, as targets for immune-mediated virus elimination, and in virion morphogenesis and secretion. Here we report the characterization of infectious HBV variant genomes that are unable to express a pre-S2 protein and which were derived from serum of a highly viremic chronic carrier. Direct sequencing of the amplified pre-S region and sequencing of 50 cloned amplified pre-S DNA fragments revealed that in all molecules, in addition to numerous nucleotide changes, there were deletions of the pre-S2 translation initiation codon and three codons 54 nucleotides downstream thereof. No pre-S2 protein and altered pre-S1 proteins were found in the serum of the patient. Cloned infectious HBV DNA genomes having the pre-S region substituted by the variant pre-S region were replication competent in cultured hepatoblastoma cells. Morphologically normal virions were efficiently secreted and were infectious for primary human hepatocyte cultures. These data demonstrate that HBV devoid of pre-S2 protein can occur in vivo as a dominant or exclusive virus population and that expression of the pre-S2 protein is not essential for HBV replication, virion morphogenesis, secretion, or in vitro infectivity.