BACKGROUND:Rotavirus vaccines, RotaTeq and Rotarix, were introduced into the Australian National Immunization Program on July 1, 2007. The simultaneous introduction in different Australian states and territories provides a unique opportunity to compare the affect of each vaccine on the types of circulating rotavirus strains. This report describes the rotavirus genotypes responsible for the hospitalization of children during the first 2-year period after vaccine introduction. METHODS:A total of 764 rotavirus-associated diarrheal cases were collected from children presenting to hospital in 10 Australian centers. Rotavirus genotype was determined using reverse transcription polymerase chain reaction assays. RESULTS:G1P8 was the dominant genotype nationally (52%), followed by G2P4 (19.8%), G9P8 (12.2%), and G3P8 (11%). Differences in the prevalence rates of G2P4 and G3P8 were seen in the various states. G2P4 strains were more prevalent in states using Rotarix, whereas G3P8 strains were more prevalent in states using RotaTeq. CONCLUSIONS:Differences in rotavirus genotypes were observed across Australia, which suggest that different immune pressures are exerted by the different vaccines, but do not necessarily imply lack of protection by either vaccine. These differences may simply be related to the variation that can occur because of natural annual fluctuation in rotavirus strain prevalence.