Hepatitis B virus (HBV) genomes have been classified into eight genotypes based on phylogenetic analysis of sequence variation. Identifying and tracking the movement of HBV genotypes is important in terms of both monitoring infection rates and predicting disease and treatment. An HBV genotyping tool has been developed that compares query sequences with position-specific scoring matrices representing the eight HBV genotypes. This tool (HBV STAR) is rapid, robust and accurate and assigns genotype based on a statistically defined scoring model. HBV STAR confidently assigned 90 % of 590 full-length HBV genomes to an HBV genotype (Z score > 2.0). Thirty-two of the residual 48 sequences were identified as non-human primate viruses and 16 sequences were identified as recombinant or putative recombinants. Receiver-Operated Characteristic (ROC) analysis was used to compare the accuracy of genotype prediction using basal core promoter sequences and surface and core genes with the accuracy achieved by using full-length sequences. A web interface to HBV STAR is available at http://www.vgb.ucl.ac.uk/ starn.shtml. © 2006 SGM.