DNA sequence variation analysis has divided varicella-zoster virus (VZV; Human herpesvirus 3) into distinct geographical clades: European, Asian, African and Japanese. These genotypes are becoming increasingly prevalent within regions atypical to their original source and there has been the suggestion of recombination between genotypes. Seventy-eight clinical isolates from hospitalized patients with varicella were collected in New South Wales, the Northern Territory, Western Australia and Victoria from 2006 to 2009. The wild-type strains and the vaccine strain (vOka) were differentiated by single nucleotide polymorphism detection using high-resolution melt analysis of five target genes (ORF1, -21, -37, -60 and -62), and by DNA sequence analysis of a 484 bp region of ORF22. Phylogenetic analysis showed that 46 % (36/78) of the clinical isolates were European clade 1 (C/E1) strains, 21 % (16/78) were European clade 3 (B/E2) strains, 12 % (9/78) were Asian/African clade 5 (A/M1) strains, 10 % (8/78) were clade 4 (J2/M2), 6 % (5/78) were clade 2 (J/J) and 5 % (4/78) belonged to the novel clade VI. No significant association was shown between VZV genotype and region, age or gender. Although European strains were most common, the results suggest an increase in African/Asian, Japanese and clade VI genotypes circulating in Australia.