Enterovirus 71 (EV71), first isolated in 1969, has been responsible for numerous outbreaks of hand, foot and mouth disease (HFMD) with a small proportion of cases associated with neurological disease. Since 1997 there has been a significant increase in both the prevalence and virulence of EV71 in the Asia-Pacific region. We have examined the genetic diversity of EV71 in a large Australian city (Sydney N.S.W.) over a nineteen-year period. We determined the VP1 gene sequence of forty-eight EV71 strains isolated between 1983 and 2001. Analysis by molecular phylogeny revealed the presence of four subgenogroups B2, B4, C1 and C2. The results indicate that the major lineage circulating in Sydney N.S.W. was subgenogroup C1 with a recent switch in dominance to B4 in 2000 and 2001