Influenza surveillance in Australia is based on laboratory isolation of influenza viruses, sentinel general practitioner reports of influenza-like illness, and absenteeism data from a major national employer. In 2006, 3,130 cases of laboratory-confirmed influenza were reported to the National Notifiable Diseases Surveillance System, which was one-third lower than in 2005. The influenza season started in mid-June, with peak activity in late August. Influenza A was the predominant type notified (71%), however influenza B activity continued to increase as a proportion of reported cases. Reports of influenza-like illness from sentinel general practitioners showed a slow but steady increase throughout the first half of the year to peak in late August. In 2006, 657 influenza isolates from Australia were antigenically analysed: 402 were A(H3N2), 24 were A(H1N1) and 231 were influenza B viruses. Continued antigenic drift was seen with the A(H3N2) viruses from the previous reference strains (A/California/7/2004 and A/New York/55/2004) and drift was also noted in some of the A(H1N1) strains from the reference/ vaccine strain A/New Caledonia/20/99, although very few A(H1N1) viruses were isolated in Australia in 2006. The B viruses isolated were predominately of the B/Victoria-lineage and similar to the reference/vaccine strain B/Malaysia/2506/2004.