The National Rotavirus Reference Centre together with collaborating laboratories Australia-wide has conducted rotavirus surveillance since June 1999. This report describes the serotypes of rotavirus strains responsible for the hospitalisation of children with acute gastroenteritis during the period 1 July 2005 to 30 June 2006. Eight hundred and forty-eight faecal samples from across Australia were examined using monoclonal antibody immunoassays, reverse transcription-polymerase chain reaction and polyacrylamide gel analysis. Serotype G1 was the dominant serotype nationally, representing 40.2 per cent of all strains, followed by serotype G4 (22.6%), serotype G9 (15.1%) and serotype G3 (14.7%). Genotype G12 strains were identified for the first time in Australia. As in previous years, there was substantial geographic variation in the prevalence of rotavirus serotypes.